Diff of the two buildlogs:

--
--- b1/build.log	2024-12-09 12:18:29.247018334 +0000
+++ b2/build.log	2024-12-09 12:45:13.094237445 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Sun Jan 11 06:21:09 -12 2026
-I: pbuilder-time-stamp: 1768155669
+I: Current time: Tue Dec 10 02:18:32 +14 2024
+I: pbuilder-time-stamp: 1733746712
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
 I: copying local configuration
@@ -35,52 +35,84 @@
 dpkg-source: info: applying python3.12_syntax_warning.patch
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/2982031/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/712969/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos1-amd64.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+'/bin/sh' -> '/bin/bash'
+lrwxrwxrwx 1 root root 9 Dec  9 12:18 /bin/sh -> /bin/bash
+I: Setting pbuilder2's login shell to /bin/bash
+I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
+I: user script /srv/workspace/pbuilder/712969/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/712969/tmp/hooks/D02_print_environment starting
 I: set
-  BUILDDIR='/build/reproducible-path'
-  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
-  BUILDUSERNAME='pbuilder1'
-  BUILD_ARCH='amd64'
-  DEBIAN_FRONTEND='noninteractive'
-  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
-  DISTRIBUTION='unstable'
-  HOME='/root'
-  HOST_ARCH='amd64'
+  BASH=/bin/sh
+  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+  BASH_ALIASES=()
+  BASH_ARGC=()
+  BASH_ARGV=()
+  BASH_CMDS=()
+  BASH_LINENO=([0]="12" [1]="0")
+  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+  BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
+  BASH_VERSION='5.2.37(1)-release'
+  BUILDDIR=/build/reproducible-path
+  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+  BUILDUSERNAME=pbuilder2
+  BUILD_ARCH=amd64
+  DEBIAN_FRONTEND=noninteractive
+  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
+  DIRSTACK=()
+  DISTRIBUTION=unstable
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=x86_64
+  HOST_ARCH=amd64
   IFS=' 	
   '
-  INVOCATION_ID='6a5a6e43c2284ba6ad504c1e570d56bc'
-  LANG='C'
-  LANGUAGE='en_US:en'
-  LC_ALL='C'
-  MAIL='/var/mail/root'
-  OPTIND='1'
-  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
-  PBCURRENTCOMMANDLINEOPERATION='build'
-  PBUILDER_OPERATION='build'
-  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
-  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
-  PBUILDER_SYSCONFDIR='/etc'
-  PPID='2982031'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=ab04347261e2427caca741b579f8016c
+  LANG=C
+  LANGUAGE=et_EE:et
+  LC_ALL=C
+  MACHTYPE=x86_64-pc-linux-gnu
+  MAIL=/var/mail/root
+  OPTERR=1
+  OPTIND=1
+  OSTYPE=linux-gnu
+  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+  PBCURRENTCOMMANDLINEOPERATION=build
+  PBUILDER_OPERATION=build
+  PBUILDER_PKGDATADIR=/usr/share/pbuilder
+  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+  PBUILDER_SYSCONFDIR=/etc
+  PIPESTATUS=([0]="0")
+  POSIXLY_CORRECT=y
+  PPID=712969
   PS4='+ '
-  PWD='/'
-  SHELL='/bin/bash'
-  SHLVL='2'
-  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.MR8995E4/pbuilderrc_qLjB --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MR8995E4/b1 --logfile b1/build.log ariba_2.14.7+ds-5.dsc'
-  SUDO_GID='111'
-  SUDO_UID='106'
-  SUDO_USER='jenkins'
-  TERM='unknown'
-  TZ='/usr/share/zoneinfo/Etc/GMT+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
-  http_proxy='http://213.165.73.152:3128'
+  PWD=/
+  SHELL=/bin/bash
+  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+  SHLVL=3
+  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.MR8995E4/pbuilderrc_azC1 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MR8995E4/b2 --logfile b2/build.log ariba_2.14.7+ds-5.dsc'
+  SUDO_GID=110
+  SUDO_UID=105
+  SUDO_USER=jenkins
+  TERM=unknown
+  TZ=/usr/share/zoneinfo/Etc/GMT-14
+  UID=0
+  USER=root
+  _='I: set'
+  http_proxy=http://46.16.76.132:3128
 I: uname -a
-  Linux ionos15-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux
+  Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux
 I: ls -l /bin
-  lrwxrwxrwx 1 root root 7 Nov 22  2024 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/2982031/tmp/hooks/D02_print_environment finished
+  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/712969/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -400,7 +432,7 @@
 Get: 240 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.3.4-1 [250 kB]
 Get: 241 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-1+b1 [178 kB]
 Get: 242 http://deb.debian.org/debian unstable/main amd64 spades amd64 3.15.5+dfsg-7 [9020 kB]
-Fetched 169 MB in 8s (20.2 MB/s)
+Fetched 169 MB in 8s (21.5 MB/s)
 debconf: delaying package configuration, since apt-utils is not installed
 Selecting previously unselected package readline-common.
 (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19965 files and directories currently installed.)
@@ -1196,8 +1228,8 @@
 Setting up tzdata (2024b-4) ...
 
 Current default time zone: 'Etc/UTC'
-Local time is now:      Sun Jan 11 18:26:18 UTC 2026.
-Universal Time is now:  Sun Jan 11 18:26:18 UTC 2026.
+Local time is now:      Mon Dec  9 12:23:07 UTC 2024.
+Universal Time is now:  Mon Dec  9 12:23:07 UTC 2024.
 Run 'dpkg-reconfigure tzdata' if you wish to change it.
 
 Setting up unicode-data (15.1.0-1) ...
@@ -1413,7 +1445,11 @@
 Building tag database...
  -> Finished parsing the build-deps
 I: Building the package
-I: Running cd /build/reproducible-path/ariba-2.14.7+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../ariba_2.14.7+ds-5_source.changes
+I: user script /srv/workspace/pbuilder/712969/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for unstable
+I: user script /srv/workspace/pbuilder/712969/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/ariba-2.14.7+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S  > ../ariba_2.14.7+ds-5_source.changes
 dpkg-buildpackage: info: source package ariba
 dpkg-buildpackage: info: source version 2.14.7+ds-5
 dpkg-buildpackage: info: source distribution unstable
@@ -1473,790 +1509,790 @@
 running build
 running build_py
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/external_progs.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/megares_zip_parser.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/flag.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/mapping.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/report_flag_expander.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/reference_data.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
 copying ariba/mlst_profile.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/card_record.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/ref_preparer.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/sequence_variant.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/read_store.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
 copying ariba/common.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/versions.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/reference_data.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/summary_cluster.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/clusters.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/read_filter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/bam_parse.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/assembly.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/histogram.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/pubmlst_ref_preparer.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/flag.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/scaffold_graph.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
 copying ariba/assembly_compare.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/faidx.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/mapping.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/vfdb_parser.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/clusters.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/assembly_variants.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/summary_cluster.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/mlst_reporter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/report.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
 copying ariba/link.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
 copying ariba/refdata_query.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/mlst_reporter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/report_filter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/summary.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/report_flag_expander.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/aln_to_metadata.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/samtools_variants.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/summary_sample.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
 copying ariba/cdhit.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/megares_data_finder.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/cluster.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/ref_genes_getter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/bam_parse.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/megares_zip_parser.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
 copying ariba/mic_plotter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/vfdb_parser.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/read_store.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/sequence_variant.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/assembly_variants.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/pubmlst_ref_preparer.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/faidx.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/pubmlst_getter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/report.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/scaffold_graph.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/read_filter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/histogram.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/tb.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/ref_genes_getter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/megares_data_finder.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
 copying ariba/ref_seq_chooser.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
 copying ariba/summary_cluster_variant.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/card_record.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/summary_sample.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/summary.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/tb.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/report_filter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/samtools_variants.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/aln_to_metadata.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
 copying ariba/sequence_metadata.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/assembly.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
-copying ariba/ref_preparer.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/external_progs.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/cluster.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/versions.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
+copying ariba/pubmlst_getter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/ref_genes_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/histogram_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/test_refdata_query.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
 copying ariba/tests/summary_sample_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/tb_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/mlst_reporter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/mlst_profile_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/megares_zip_parser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/summary_cluster_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/card_record_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/versions_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/clusters_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
 copying ariba/tests/read_store_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/link_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/mic_plotter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/reference_data_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
 copying ariba/tests/scaffold_graph_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/summary_cluster_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/histogram_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/report_flag_expander_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/summary_cluster_variant_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
 copying ariba/tests/aln_to_metadata_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/megares_zip_parser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/bam_parse_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/flag_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/megares_data_finder_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/pubmlst_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/samtools_variants_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/clusters_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/vfdb_parser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/cluster_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/assembly_compare_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/versions_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/summary_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/read_filter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/report_filter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/external_progs_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
 copying ariba/tests/ref_preparer_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/cdhit_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/tb_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/common_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
 copying ariba/tests/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/external_progs_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/samtools_variants_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/link_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/pubmlst_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/assembly_compare_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/flag_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/cluster_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/assembly_variants_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
 copying ariba/tests/assembly_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/faidx_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/summary_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/read_filter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/pubmlst_ref_preparer_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/sequence_metadata_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
 copying ariba/tests/mapping_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/mlst_profile_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/sequence_variant_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/test_refdata_query.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/megares_data_finder_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/mic_plotter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/sequence_metadata_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/faidx_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/ref_genes_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
 copying ariba/tests/ncbi_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/assembly_variants_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/summary_cluster_variant_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/common_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
 copying ariba/tests/ref_seq_chooser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/report_flag_expander_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/mlst_reporter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/card_record_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
-copying ariba/tests/report_filter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/bam_parse_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/cdhit_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/reference_data_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/sequence_variant_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/vfdb_parser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
+copying ariba/tests/pubmlst_ref_preparer_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
+copying ariba/tasks/expandflag.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
+copying ariba/tasks/micplot.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
+copying ariba/tasks/pubmlstget.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
+copying ariba/tasks/refquery.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
+copying ariba/tasks/aln2meta.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
 copying ariba/tasks/flag.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
-copying ariba/tasks/version.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
 copying ariba/tasks/prepareref_tb.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
+copying ariba/tasks/version.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
+copying ariba/tasks/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
 copying ariba/tasks/getref.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
-copying ariba/tasks/refquery.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
-copying ariba/tasks/aln2meta.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
+copying ariba/tasks/reportfilter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
 copying ariba/tasks/test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
 copying ariba/tasks/pubmlstspecies.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
 copying ariba/tasks/summary.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
-copying ariba/tasks/run.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
-copying ariba/tasks/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
-copying ariba/tasks/expandflag.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
-copying ariba/tasks/reportfilter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
 copying ariba/tasks/prepareref.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
-copying ariba/tasks/micplot.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
-copying ariba/tasks/pubmlstget.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
+copying ariba/tasks/run.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data
-copying ariba/test_run_data/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data
-copying ariba/test_run_data/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data
-copying ariba/test_run_data/metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data
 copying ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data
+copying ariba/test_run_data/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data
+copying ariba/test_run_data/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data
 copying ariba/test_run_data/ref_seqs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data
+copying ariba/test_run_data/metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
-copying ariba/tb_data/panel.20190102.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
 copying ariba/tb_data/panel.20181221.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
-copying ariba/tb_data/panel.20190102.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
 copying ariba/tb_data/panel.20181221.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
-copying ariba/tb_data/panel.20181115.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
-copying ariba/tb_data/NC_000962.3.gb -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
+copying ariba/tb_data/panel.20190102.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
 copying ariba/tb_data/NC_000962.3.fa.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
+copying ariba/tb_data/panel.20181115.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
 copying ariba/tb_data/panel.20181115.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
+copying ariba/tb_data/NC_000962.3.gb -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
+copying ariba/tb_data/panel.20190102.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_fasta_file.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads.no_link_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/test_common_cat_files.in.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_rename_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_test_init.fofn -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/assembly_test_check_spades_log_file.log.bad -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/graph_test_update_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_count_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_preparer_test_run.in.3.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_preparer_test_run.in.4.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_check_not_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_test_run.in.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_init_fails.empty.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_profile_test.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/summary_test_whole_run.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_check_too_long.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_get_variants.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_cat_genes_match_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/vfdb_parser_test_run.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_fix_out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_run_fermilite.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/clusters_test_write_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/graph_test_update_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/ref_preparer_test_run.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_init_refdata.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_rename_sequences.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_rename_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/report_filter_test_init_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_test_whole_run.out.csv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_count_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_init_fails.empty.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_init_ok.rename.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_init_ok.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_run_fermilite.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_sequence.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_parse.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/refdata_query_prepareref.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/pubmlst_rename_seqs.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.profile.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_sample_test_load_file.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_dummy_db.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_init_fails.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_init_ok.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/report_filter_test_init_bad.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads.make_link_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_fix_out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/tb_genbank_to_gene_coords.gb -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads.no_link_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_parse.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_fix_out.rename -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_init_ok.params.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_sequence.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_sequence.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/test_common_cat_files.in.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/report_filter_test_load_report_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/dummy.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_parse.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads.no_link_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_to_matrix.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/vfdb_parser_test_run.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_fix_in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/aln_to_metadata_run_coding.out.cluster -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/megares_zip_parser_load_annotations.csv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_init_ok.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_sort_file.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_bowtie2_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_profile_test.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/mapping_test_bowtie2_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_rename_sequences.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads.make_link.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_init_ok.params.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_test_load_fofn -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/megares_zip_parse_extract_files_ok.zip -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_get_reads.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/report_filter_test_run.expected.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads.no_link.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_sequence_type.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_preparer_test_run.in.1.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/test_common_cat_files.in.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/report_filter_test_init_bad.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_dummy_db.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_remove_bad_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/graph_test_update_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_parse.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mic_plotter_load_summary_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_test_write_distance_matrix.distances -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_fake_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/tb_report_to_resistance_dict.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_preparer_test_run.in.3.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/report_flag_expander.run.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads.make_link_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_test_run.in.read_store -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_parse.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_bowtie2_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_dummy_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_sample_test_var_groups.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/test_common_cat_files.in.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_to_matrix.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_preparer_test_run.in.2.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_profile_test.init.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_rename_sequences.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_sequence.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_cat_genes_match_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_dummy_db.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_rename_sequences.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_fix_in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_check_ok.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_test_run.in.read_store -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_profile_test.init.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/reference_data_load_all_metadata_tsvs.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_parse.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/graph_test_write_all_links_to_file.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/pubmlst_getter.dbases.xml -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_check_too_short.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/refdata_query_prepareref.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_test_write_distance_matrix.distances -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads.no_link.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_sequence_type.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_sample_test_var_groups.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.profile.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.smi -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_run_fermilite.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/report_filter_test_load_report_bad.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_fix_out.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_run_fermilite.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_init_refdata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads.make_link_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/report_filter_test_init_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_sam_to_fastq.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/report_filter_test_run.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/cluster_test_full_run_insert_codon.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/vfdb_parser_test_run.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_test_run.in.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/tb_report_to_resistance_dict.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mic_plotter_load_summary_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/report_filter_test_load_report_bad.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_test_load_input_files.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_fix_out.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_get_variants.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/graph_test_write_all_links_to_file.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_test_whole_run.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_check_not_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads.make_link_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_clean.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_fix_out.rename -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_test_load_input_files.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/clusters_test_write_mlst_reports.ariba.report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/report_filter_test_write_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_sort_file.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_test_whole_run.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_test_init.fofn -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_sam_to_fastq.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_init_fails.empty.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/test_common_cat_files.in.3 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/report_flag_expander.run.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/tb_genbank_to_gene_coords.gb -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_test_load_input_files.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_sample_test_load_file.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_fix_out.removed.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_count_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_count_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_load_data_info_file -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_fasta_file.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/report_flag_expander.run.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/refdata_query_prepareref.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_test_load_fofn -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_dummy_db.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_init_fails.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/mic_plotter_load_mic_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_get_reads.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_init_refdata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/vfdb_parser_test_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_sequence_type.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_compress_and_index_file.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads.no_link_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_preparer_test_run.in.4.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_remove_bad_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_sort_file.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/mapping_test_bowtie2_unsorted.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/report_filter_test_run.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/reference_data_load_all_fasta_files.in.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/report_filter_test_write_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/graph_test_update_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/report_filter_test_run.expected.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/test_common_cat_files.in.3 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_clean.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_dummy_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/vfdb_parser_test_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_to_matrix.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_check_ok.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/dummy.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/report_filter_test_load_report_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_sequence_type.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/pubmlst_rename_seqs.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_load_data_info_file -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_dummy_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_preparer_test_run.in.2.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/test_common_cat_files.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_init_ok.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_dummy_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_fix_out.removed.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_fake_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_compress_and_index_file.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_init_ok.rename.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_check_too_short.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_init_refdata.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/pubmlst_getter.dbases.xml -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_sort_file.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_init_fails.empty.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_run_fermilite.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads.make_link.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_run_fermilite.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_preparer_test_run.in.1.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/test_common_cat_files.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_test_whole_run.out.csv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_check_too_long.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/megares_zip_parser_load_annotations.csv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_to_matrix.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_test_load_input_files.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
-copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
-copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
-copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
-copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
-copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
 copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
 copying ariba/tests/data/refdata_query_prepareref/00.rename_info -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
-copying ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
+copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
+copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
+copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
+copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
 copying ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
+copying ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
+copying ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
+copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
+copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
+copying ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
 copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
 copying ariba/tests/data/refdata_query_prepareref/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
-copying ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
-copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
-copying ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding
-copying ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding
-copying ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding
 copying ariba/tests/data/cluster_test_full_run_ok_non_coding/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding
+copying ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding
+copying ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
-copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
-copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
 copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
+copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
+copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
-copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
-copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
+copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
 copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
-copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
+copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
+copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
 copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
-copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
-copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
 copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
+copying ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
+copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
+copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
+copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
+copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
 copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
 copying ariba/tests/data/ref_preparer_test_run.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
-copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
-copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
-copying ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
 copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
 copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.rename_info -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
 copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
 copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
 copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
-copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
-copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
-copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
-copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
-copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
 copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
+copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
 copying ariba/tests/data/clusters_run_with_tb.ref/00.params.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
+copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
+copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
+copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
 copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
+copying ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
+copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
+copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
+copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
 copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
 copying ariba/tests/data/clusters_run_with_tb.ref/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
-copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
-copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
-copying ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
-copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
-copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
-copying ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
 copying ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
+copying ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
+copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
+copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
-copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
-copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
 copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
+copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
+copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail
-copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail
-copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail
 copying ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail
+copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail
+copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
-copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
-copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
 copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
+copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
+copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence
-copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence
-copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence
 copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence
+copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence
+copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
-copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
-copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
-copying ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
 copying ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
+copying ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
+copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
+copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
-copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
-copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
 copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
+copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
+copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly
-copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly
-copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly
 copying ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly
+copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly
+copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
-copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
 copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene2.tfa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
+copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
 copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/profile.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa
-copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa
 copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa
+copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
-copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
-copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
 copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
+copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
+copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
 copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
 copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
 copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
 copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
 copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files
+copying ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files
 copying ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files
 copying ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files
-copying ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
-copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
-copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
 copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
+copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
+copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
-copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
-copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
 copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
+copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
+copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2
-copying ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2
 copying ariba/tests/data/cluster_test_init_no_reads_2/genes.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2
+copying ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
 copying ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
 copying ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
-copying ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
-copying ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
 copying ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
+copying ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
+copying ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
-copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
-copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
 copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
+copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
+copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
-copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
-copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
 copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
+copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
+copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
-copying ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
-copying ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
 copying ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
+copying ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
+copying ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
-copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
-copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
-copying ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
 copying ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
+copying ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
+copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
+copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1
-copying ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1
 copying ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1
+copying ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
-copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
-copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
 copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
+copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
+copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
 running build_ext
 building 'minimap_ariba' extension
 creating build/temp.linux-x86_64-cpython-313/ariba/ext
@@ -2280,790 +2316,790 @@
 running build
 running build_py
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/external_progs.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/megares_zip_parser.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/flag.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/mapping.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/report_flag_expander.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/reference_data.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
 copying ariba/mlst_profile.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/card_record.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/ref_preparer.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/sequence_variant.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/read_store.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
 copying ariba/common.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/versions.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/reference_data.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/summary_cluster.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/clusters.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/read_filter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/bam_parse.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/assembly.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/histogram.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/pubmlst_ref_preparer.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/flag.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/scaffold_graph.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
 copying ariba/assembly_compare.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/faidx.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/mapping.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/vfdb_parser.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/clusters.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/assembly_variants.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/summary_cluster.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/mlst_reporter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/report.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
 copying ariba/link.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
 copying ariba/refdata_query.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/mlst_reporter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/report_filter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/summary.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/report_flag_expander.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/aln_to_metadata.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/samtools_variants.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/summary_sample.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
 copying ariba/cdhit.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/megares_data_finder.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/cluster.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/ref_genes_getter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/bam_parse.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/megares_zip_parser.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
 copying ariba/mic_plotter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/vfdb_parser.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/read_store.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/sequence_variant.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/assembly_variants.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/pubmlst_ref_preparer.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/faidx.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/pubmlst_getter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/report.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/scaffold_graph.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/read_filter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/histogram.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/tb.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/ref_genes_getter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/megares_data_finder.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
 copying ariba/ref_seq_chooser.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
 copying ariba/summary_cluster_variant.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/card_record.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/summary_sample.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/summary.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/tb.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/report_filter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/samtools_variants.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/aln_to_metadata.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
 copying ariba/sequence_metadata.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/assembly.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
-copying ariba/ref_preparer.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/external_progs.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/cluster.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/versions.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
+copying ariba/pubmlst_getter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/ref_genes_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/histogram_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/test_refdata_query.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
 copying ariba/tests/summary_sample_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/tb_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/mlst_reporter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/mlst_profile_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/megares_zip_parser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/summary_cluster_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/card_record_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/versions_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/clusters_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
 copying ariba/tests/read_store_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/link_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/mic_plotter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/reference_data_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
 copying ariba/tests/scaffold_graph_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/summary_cluster_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/histogram_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/report_flag_expander_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/summary_cluster_variant_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
 copying ariba/tests/aln_to_metadata_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/megares_zip_parser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/bam_parse_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/flag_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/megares_data_finder_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/pubmlst_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/samtools_variants_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/clusters_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/vfdb_parser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/cluster_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/assembly_compare_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/versions_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/summary_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/read_filter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/report_filter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/external_progs_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
 copying ariba/tests/ref_preparer_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/cdhit_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/tb_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/common_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
 copying ariba/tests/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/external_progs_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/samtools_variants_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/link_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/pubmlst_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/assembly_compare_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/flag_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/cluster_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/assembly_variants_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
 copying ariba/tests/assembly_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/faidx_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/summary_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/read_filter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/pubmlst_ref_preparer_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/sequence_metadata_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
 copying ariba/tests/mapping_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/mlst_profile_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/sequence_variant_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/test_refdata_query.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/megares_data_finder_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/mic_plotter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/sequence_metadata_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/faidx_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/ref_genes_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
 copying ariba/tests/ncbi_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/assembly_variants_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/summary_cluster_variant_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/common_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
 copying ariba/tests/ref_seq_chooser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/report_flag_expander_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/mlst_reporter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/card_record_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
-copying ariba/tests/report_filter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/bam_parse_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/cdhit_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/reference_data_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/sequence_variant_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/vfdb_parser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
+copying ariba/tests/pubmlst_ref_preparer_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
+copying ariba/tasks/expandflag.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
+copying ariba/tasks/micplot.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
+copying ariba/tasks/pubmlstget.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
+copying ariba/tasks/refquery.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
+copying ariba/tasks/aln2meta.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
 copying ariba/tasks/flag.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
-copying ariba/tasks/version.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
 copying ariba/tasks/prepareref_tb.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
+copying ariba/tasks/version.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
+copying ariba/tasks/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
 copying ariba/tasks/getref.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
-copying ariba/tasks/refquery.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
-copying ariba/tasks/aln2meta.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
+copying ariba/tasks/reportfilter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
 copying ariba/tasks/test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
 copying ariba/tasks/pubmlstspecies.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
 copying ariba/tasks/summary.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
-copying ariba/tasks/run.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
-copying ariba/tasks/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
-copying ariba/tasks/expandflag.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
-copying ariba/tasks/reportfilter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
 copying ariba/tasks/prepareref.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
-copying ariba/tasks/micplot.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
-copying ariba/tasks/pubmlstget.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
+copying ariba/tasks/run.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data
-copying ariba/test_run_data/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data
-copying ariba/test_run_data/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data
-copying ariba/test_run_data/metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data
 copying ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data
+copying ariba/test_run_data/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data
+copying ariba/test_run_data/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data
 copying ariba/test_run_data/ref_seqs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data
+copying ariba/test_run_data/metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
-copying ariba/tb_data/panel.20190102.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
 copying ariba/tb_data/panel.20181221.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
-copying ariba/tb_data/panel.20190102.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
 copying ariba/tb_data/panel.20181221.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
-copying ariba/tb_data/panel.20181115.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
-copying ariba/tb_data/NC_000962.3.gb -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
+copying ariba/tb_data/panel.20190102.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
 copying ariba/tb_data/NC_000962.3.fa.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
+copying ariba/tb_data/panel.20181115.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
 copying ariba/tb_data/panel.20181115.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
+copying ariba/tb_data/NC_000962.3.gb -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
+copying ariba/tb_data/panel.20190102.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_fasta_file.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads.no_link_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/test_common_cat_files.in.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_rename_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_test_init.fofn -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/assembly_test_check_spades_log_file.log.bad -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/graph_test_update_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_count_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_preparer_test_run.in.3.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_preparer_test_run.in.4.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_check_not_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_test_run.in.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_init_fails.empty.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_profile_test.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/summary_test_whole_run.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_check_too_long.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_get_variants.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_cat_genes_match_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/vfdb_parser_test_run.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_fix_out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_run_fermilite.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/clusters_test_write_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/graph_test_update_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/ref_preparer_test_run.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_init_refdata.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_rename_sequences.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_rename_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/report_filter_test_init_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_test_whole_run.out.csv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_count_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_init_fails.empty.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_init_ok.rename.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_init_ok.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_run_fermilite.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_sequence.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_parse.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/refdata_query_prepareref.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/pubmlst_rename_seqs.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.profile.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_sample_test_load_file.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_dummy_db.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_init_fails.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_init_ok.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/report_filter_test_init_bad.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads.make_link_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_fix_out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/tb_genbank_to_gene_coords.gb -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads.no_link_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_parse.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_fix_out.rename -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_init_ok.params.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_sequence.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_sequence.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/test_common_cat_files.in.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/report_filter_test_load_report_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/dummy.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_parse.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads.no_link_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_to_matrix.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/vfdb_parser_test_run.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_fix_in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/aln_to_metadata_run_coding.out.cluster -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/megares_zip_parser_load_annotations.csv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_init_ok.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_sort_file.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_bowtie2_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_profile_test.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/mapping_test_bowtie2_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_rename_sequences.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads.make_link.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_init_ok.params.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_test_load_fofn -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/megares_zip_parse_extract_files_ok.zip -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_get_reads.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/report_filter_test_run.expected.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads.no_link.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_sequence_type.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_preparer_test_run.in.1.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/test_common_cat_files.in.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/report_filter_test_init_bad.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_dummy_db.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_remove_bad_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/graph_test_update_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_parse.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mic_plotter_load_summary_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_test_write_distance_matrix.distances -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_fake_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/tb_report_to_resistance_dict.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_preparer_test_run.in.3.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/report_flag_expander.run.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads.make_link_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_test_run.in.read_store -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_parse.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_bowtie2_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_dummy_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_sample_test_var_groups.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/test_common_cat_files.in.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_to_matrix.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_preparer_test_run.in.2.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_profile_test.init.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_rename_sequences.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_sequence.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_cat_genes_match_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_dummy_db.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_rename_sequences.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_fix_in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_check_ok.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_test_run.in.read_store -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_profile_test.init.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/reference_data_load_all_metadata_tsvs.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_parse.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/graph_test_write_all_links_to_file.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/pubmlst_getter.dbases.xml -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_check_too_short.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/refdata_query_prepareref.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_test_write_distance_matrix.distances -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads.no_link.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_sequence_type.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_sample_test_var_groups.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.profile.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.smi -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_run_fermilite.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/report_filter_test_load_report_bad.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_fix_out.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_run_fermilite.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_init_refdata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads.make_link_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/report_filter_test_init_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_sam_to_fastq.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/report_filter_test_run.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/cluster_test_full_run_insert_codon.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/vfdb_parser_test_run.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_test_run.in.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/tb_report_to_resistance_dict.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mic_plotter_load_summary_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/report_filter_test_load_report_bad.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_test_load_input_files.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_fix_out.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_get_variants.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/graph_test_write_all_links_to_file.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_test_whole_run.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_check_not_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads.make_link_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_clean.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_fix_out.rename -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_test_load_input_files.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/clusters_test_write_mlst_reports.ariba.report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/report_filter_test_write_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_sort_file.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_test_whole_run.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_test_init.fofn -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mapping_test_sam_to_fastq.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_init_fails.empty.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/test_common_cat_files.in.3 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/report_flag_expander.run.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/tb_genbank_to_gene_coords.gb -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_test_load_input_files.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_sample_test_load_file.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_fix_out.removed.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_count_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_count_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_load_data_info_file -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_fasta_file.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/report_flag_expander.run.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/refdata_query_prepareref.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_test_load_fofn -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_dummy_db.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_init_fails.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/mic_plotter_load_mic_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_get_reads.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_init_refdata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/vfdb_parser_test_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_sequence_type.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_compress_and_index_file.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads.no_link_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_preparer_test_run.in.4.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_remove_bad_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_sort_file.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/mapping_test_bowtie2_unsorted.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/report_filter_test_run.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/reference_data_load_all_fasta_files.in.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/report_filter_test_write_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/graph_test_update_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/report_filter_test_run.expected.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/test_common_cat_files.in.3 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_clean.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_dummy_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/vfdb_parser_test_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/summary_to_matrix.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_check_ok.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/dummy.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/report_filter_test_load_report_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/link_test_init.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_sequence_type.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/pubmlst_rename_seqs.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_load_data_info_file -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_dummy_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_preparer_test_run.in.2.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/test_common_cat_files.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_init_ok.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_test_dummy_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/refcheck_test_fix_out.removed.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_fake_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/read_store_test_compress_and_index_file.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_init_ok.rename.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_check_too_short.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_init_refdata.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/pubmlst_getter.dbases.xml -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_sort_file.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_init_fails.empty.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_run_fermilite.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
-copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/link_test_init.reads.make_link.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_run_fermilite.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_preparer_test_run.in.1.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/test_common_cat_files.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_test_whole_run.out.csv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/refcheck_test_check_too_long.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/megares_zip_parser_load_annotations.csv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_to_matrix.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/summary_test_load_input_files.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
+copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
-copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
-copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
-copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
-copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
-copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
 copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
 copying ariba/tests/data/refdata_query_prepareref/00.rename_info -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
-copying ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
+copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
+copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
+copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
+copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
 copying ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
+copying ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
+copying ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
+copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
+copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
+copying ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
 copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
 copying ariba/tests/data/refdata_query_prepareref/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
-copying ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
-copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
-copying ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding
-copying ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding
-copying ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding
 copying ariba/tests/data/cluster_test_full_run_ok_non_coding/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding
+copying ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding
+copying ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
-copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
-copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
 copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
+copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
+copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
-copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
-copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
+copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
 copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
-copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
+copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
+copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
 copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
-copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
-copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
 copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
+copying ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
+copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
+copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
+copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
+copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
 copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
 copying ariba/tests/data/ref_preparer_test_run.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
-copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
-copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
-copying ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
 copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
 copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.rename_info -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
 copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
 copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
 copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
-copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
-copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
-copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
-copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
-copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
 copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
+copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
 copying ariba/tests/data/clusters_run_with_tb.ref/00.params.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
+copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
+copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
+copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
 copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
+copying ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
+copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
+copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
+copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
 copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
 copying ariba/tests/data/clusters_run_with_tb.ref/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
-copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
-copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
-copying ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
-copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
-copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
-copying ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
 copying ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
+copying ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
+copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
+copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
-copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
-copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
 copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
+copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
+copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail
-copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail
-copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail
 copying ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail
+copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail
+copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
-copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
-copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
 copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
+copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
+copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence
-copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence
-copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence
 copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence
+copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence
+copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
-copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
-copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
-copying ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
 copying ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
+copying ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
+copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
+copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
-copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
-copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
 copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
+copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
+copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly
-copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly
-copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly
 copying ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly
+copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly
+copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
-copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
 copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene2.tfa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
+copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
 copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/profile.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa
-copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa
 copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa
+copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
-copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
-copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
 copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
+copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
+copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
 copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
 copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
 copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
 copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
 copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files
+copying ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files
 copying ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files
 copying ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files
-copying ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
-copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
-copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
 copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
+copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
+copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
-copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
-copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
 copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
+copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
+copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2
-copying ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2
 copying ariba/tests/data/cluster_test_init_no_reads_2/genes.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2
+copying ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
 copying ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
 copying ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
-copying ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
-copying ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
 copying ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
+copying ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
+copying ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
-copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
-copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
 copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
+copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
+copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
-copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
-copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
 copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
+copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
+copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
-copying ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
-copying ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
 copying ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
+copying ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
+copying ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
-copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
+copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
-copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
-copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
-copying ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
 copying ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
+copying ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
+copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
+copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1
-copying ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1
 copying ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1
+copying ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1
 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
-copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
-copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
 copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
+copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
+copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
 running build_ext
 building 'minimap_ariba' extension
 creating build/temp.linux-x86_64-cpython-312/ariba/ext
@@ -3137,7 +3173,7 @@
     from pkg_resources import get_distribution
 
 ../../../../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3
-  /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'locate_file', 'read_text'}
+  /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'read_text', 'locate_file'}
     __version__ = Distribution().from_name('pyfastaq').version
 
 .pybuild/cpython3_3.13_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours
@@ -3151,7 +3187,7 @@
     cmap = cmx.get_cmap(colormap)
 
 -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
-========== 355 passed, 1 deselected, 6 warnings in 186.30s (0:03:06) ===========
+========== 355 passed, 1 deselected, 6 warnings in 450.41s (0:07:30) ===========
 I: pybuild base:311: cd /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build; python3.12 -m pytest 
 ============================= test session starts ==============================
 platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0
@@ -3209,7 +3245,7 @@
     from pkg_resources import get_distribution
 
 ../../../../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3
-  /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'locate_file', 'read_text'}
+  /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'read_text', 'locate_file'}
     __version__ = Distribution().from_name('pyfastaq').version
 
 .pybuild/cpython3_3.12_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours
@@ -3223,7 +3259,7 @@
     cmap = cmx.get_cmap(colormap)
 
 -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
-================= 356 passed, 6 warnings in 203.34s (0:03:23) ==================
+================= 356 passed, 6 warnings in 252.28s (0:04:12) ==================
    create-stamp debian/debhelper-build-stamp
    dh_testroot -O--buildsystem=pybuild
    dh_prep -O--buildsystem=pybuild
@@ -3254,1008 +3290,1008 @@
 running install_lib
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/minimap_ariba.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/fermilite_ariba.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/vcfcall_ariba.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/external_progs.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/megares_zip_parser.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/flag.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/mapping.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/report_flag_expander.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/reference_data.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/mlst_profile.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/card_record.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/ref_preparer.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/sequence_variant.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/report_filter.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/reference_data.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/card_record.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/report.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/scaffold_graph.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/ref_genes_getter.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/assembly.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/common.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/summary_sample.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/mic_plotter.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/ref_seq_chooser.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/summary.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/versions.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/megares_data_finder.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/vfdb_parser.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/sequence_variant.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/tb.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/sequence_metadata.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/read_store.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/aln_to_metadata.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/link.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/histogram.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/samtools_variants.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/mlst_reporter.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/clusters.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/report_flag_expander.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/pubmlst_ref_preparer.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/refdata_query.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/flag.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/pubmlst_getter.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/external_progs.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/read_filter.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/mapping.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/ref_preparer.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/megares_zip_parser.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/cdhit.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/mlst_profile.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/assembly_compare.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/summary_cluster_variant.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/bam_parse.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/summary_cluster.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/faidx.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/cluster.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/assembly_variants.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/read_store.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/common.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/read_filter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/bam_parse.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/test_run_data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/test_run_data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/test_run_data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data/metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/test_run_data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/test_run_data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/test_run_data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/test_run_data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data/ref_seqs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/test_run_data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/mlst_profile.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/common.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data/metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/test_run_data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/assembly.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/histogram.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/pubmlst_ref_preparer.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/flag.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/scaffold_graph.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/assembly_compare.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/faidx.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/mapping.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/vfdb_parser.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/clusters.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/assembly_variants.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/summary_cluster.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/ref_genes_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/histogram_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/test_refdata_query.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/summary_sample_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/read_store_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/link_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/mic_plotter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/reference_data_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/scaffold_graph_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/summary_cluster_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/aln_to_metadata_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/tb_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/mlst_reporter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/mlst_profile_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/mlst_profile_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/versions_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/link_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/cluster_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/reference_data_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/read_filter_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/ref_seq_chooser_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/summary_sample_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/assembly_compare_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/external_progs_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/test_refdata_query.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/scaffold_graph_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/aln_to_metadata_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/summary_cluster_variant_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/summary_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/ncbi_getter_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/common_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/test_refdata_query.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/report_filter_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/tb_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/sequence_metadata_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/assembly_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/mlst_reporter_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/card_record_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/clusters_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/faidx_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/histogram_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/link_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/versions_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/report_flag_expander_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/sequence_variant_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/assembly_compare_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/ref_preparer_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/external_progs_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/mic_plotter_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/read_store_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/mlst_profile_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/tb_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/samtools_variants_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/summary_sample_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/ref_seq_chooser_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/vfdb_parser_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/summary_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/cdhit_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/reference_data_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/assembly_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/read_filter_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/pubmlst_getter_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/bam_parse_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/clusters_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/pubmlst_ref_preparer_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/summary_cluster_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/summary_cluster_variant_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/faidx_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/sequence_variant_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/mapping_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/megares_data_finder_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/ref_genes_getter_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/samtools_variants_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/mlst_reporter_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/summary_cluster_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/cluster_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/megares_zip_parser_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/ref_preparer_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/report_flag_expander_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/card_record_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/mic_plotter_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/aln_to_metadata_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/common_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/pubmlst_ref_preparer_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/assembly_variants_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/cdhit_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/report_filter_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/sequence_metadata_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/mapping_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/flag_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/ref_genes_getter_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/bam_parse_test.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/megares_zip_parser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/summary_cluster_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/card_record_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/versions_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/clusters_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/read_store_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/scaffold_graph_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/histogram_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/report_flag_expander_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/summary_cluster_variant_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/aln_to_metadata_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/summary_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/read_filter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/report_filter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/external_progs_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/ref_preparer_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/samtools_variants_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/link_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/pubmlst_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/assembly_compare_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/flag_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/cluster_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/assembly_variants_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/assembly_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/mapping_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/test_refdata_query.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/megares_data_finder_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/mic_plotter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/sequence_metadata_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/faidx_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/ref_genes_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_fasta_file.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads.no_link_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/test_common_cat_files.in.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_rename_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_test_init.fofn -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_check_spades_log_file.log.bad -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/graph_test_update_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/megares_zip_parser_write_files
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/megares_zip_parser_write_files
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/megares_zip_parser_write_files
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/megares_zip_parser_write_files
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_count_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.in.3.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.in.4.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_check_not_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_test_run.in.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_init_fails.empty.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_profile_test.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_test_whole_run.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_check_too_long.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.vcf -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_cat_genes_match_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.rename_info -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/vfdb_parser_test_run.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_fix_out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_run_fermilite.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_write_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/graph_test_update_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_refdata.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_rename_sequences.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_rename_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/report_filter_test_init_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_test_whole_run.out.csv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_count_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_init_fails.empty.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_init_ok.rename.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_init_ok.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_run_fermilite.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_sequence.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_init_ok.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/report_filter_test_init_bad.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads.make_link_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_fix_out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/tb_genbank_to_gene_coords.gb -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads.no_link_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_parse.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_fix_out.rename -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_init_ok.params.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_sequence.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_sequence.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/test_common_cat_files.in.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/report_filter_test_load_report_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/dummy.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.cluster -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_bowtie2_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parse_extract_files_ok.zip -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_rename_seqs.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.profile.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/00.rename_info -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_sample_test_load_file.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_dummy_db.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_init_fails.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_parse.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads.no_link_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_to_matrix.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/vfdb_parser_test_run.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_fix_in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.cluster -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_load_annotations.csv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_init_ok.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_sort_file.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_bowtie2_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_profile_test.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_bowtie2_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_rename_sequences.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads.make_link.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_init_ok.params.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_test_load_fofn -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parse_extract_files_ok.zip -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_get_reads.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/report_filter_test_run.expected.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads.no_link.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_sequence_type.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.in.1.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/test_common_cat_files.in.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/report_filter_test_init_bad.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_dummy_db.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_remove_bad_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/graph_test_update_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_parse.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_load_summary_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_test_write_distance_matrix.distances -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_fake_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/tb_report_to_resistance_dict.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.in.3.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/report_flag_expander.run.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads.make_link_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_test_run.in.read_store -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/report_flag_expander.run.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_parse.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_bowtie2_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_dummy_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_sample_test_var_groups.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/test_common_cat_files.in.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_to_matrix.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.in.2.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_profile_test.init.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_rename_sequences.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_sequence.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_cat_genes_match_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_dummy_db.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_rename_sequences.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_fix_in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_check_ok.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_test_run.in.read_store -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_profile_test.init.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_all_metadata_tsvs.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_parse.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/graph_test_write_all_links_to_file.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_getter.dbases.xml -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_check_too_short.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_test_write_distance_matrix.distances -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads.no_link.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_sequence_type.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_sample_test_var_groups.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.profile.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.smi -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_run_fermilite.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/report_filter_test_init_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_sam_to_fastq.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/report_filter_test_run.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/vfdb_parser_test_run.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2/genes.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/report_filter_test_load_report_bad.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_test_load_input_files.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_fix_out.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_run_fermilite.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_refdata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads.make_link_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_test_run.in.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/tb_report_to_resistance_dict.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_load_summary_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.vcf -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/graph_test_write_all_links_to_file.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_test_whole_run.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_check_not_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads.make_link_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_clean.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_fix_out.rename -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_test_load_input_files.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.ariba.report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/report_filter_test_write_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_sort_file.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_test_whole_run.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_test_init.fofn -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_sam_to_fastq.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_init_fails.empty.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/test_common_cat_files.in.3 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/report_flag_expander.run.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/tb_genbank_to_gene_coords.gb -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_test_load_input_files.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_sample_test_load_file.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_fix_out.removed.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_count_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_count_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_load_data_info_file -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_fasta_file.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/report_flag_expander.run.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_test_load_fofn -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_dummy_db.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_init_fails.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_load_mic_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_bowtie2_unsorted.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/report_filter_test_run.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_all_fasta_files.in.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_get_reads.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_refdata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/vfdb_parser_test_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_to_matrix.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_check_ok.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/dummy.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/report_filter_test_load_report_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_sequence_type.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_sequence_type.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_compress_and_index_file.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads.no_link_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.in.4.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_remove_bad_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_sort_file.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_bowtie2_unsorted.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.params.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_all_fasta_files.in.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/report_filter_test_write_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/graph_test_update_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/report_filter_test_run.expected.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene2.tfa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/profile.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.in.2.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/test_common_cat_files.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.rename_info -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_init_ok.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/test_common_cat_files.in.3 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_clean.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_dummy_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_fix_out.removed.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_fake_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_compress_and_index_file.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/megares_zip_parser_write_files
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/megares_zip_parser_write_files
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/megares_zip_parser_write_files
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/megares_zip_parser_write_files
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_rename_seqs.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_load_data_info_file -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_dummy_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_init_ok.rename.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_check_too_short.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_refdata.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_getter.dbases.xml -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_sort_file.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_init_fails.empty.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_run_fermilite.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/link_test_init.reads.make_link.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_run_fermilite.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.in.1.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/test_common_cat_files.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_test_whole_run.out.csv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refcheck_test_check_too_long.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_load_annotations.csv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_to_matrix.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/summary_test_load_input_files.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/ncbi_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/common_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/ref_seq_chooser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/bam_parse_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/flag_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/megares_data_finder_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/pubmlst_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/samtools_variants_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/clusters_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/vfdb_parser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/cluster_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/assembly_compare_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/versions_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/ref_preparer_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/cdhit_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/tb_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/common_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/external_progs_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/assembly_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/faidx_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/summary_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/read_filter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/pubmlst_ref_preparer_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/sequence_metadata_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/mapping_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/mlst_profile_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/reference_data_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/sequence_variant_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/ncbi_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/assembly_variants_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/summary_cluster_variant_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/ref_seq_chooser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/report_flag_expander_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/mlst_reporter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/card_record_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/report_filter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/samtools_variants.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/summary.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/assembly_variants.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/cdhit.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/bam_parse.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/reference_data.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/ref_preparer.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/pubmlst_getter.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/histogram.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/common.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/mlst_profile.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/megares_zip_parser.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/mapping.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/megares_data_finder.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/vfdb_parser.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/tb.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/report_flag_expander.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/mlst_reporter.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/aln_to_metadata.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/summary_sample.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/assembly_compare.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/refdata_query.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/cluster.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/report_filter.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/versions.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/external_progs.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/link.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/report.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/clusters.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/ref_seq_chooser.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/card_record.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/assembly.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/scaffold_graph.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/faidx.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/sequence_metadata.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/summary_cluster.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/mic_plotter.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/pubmlst_ref_preparer.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/sequence_variant.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/read_store.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/ref_genes_getter.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/flag.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/summary_cluster_variant.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__pycache__/read_filter.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/versions.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/reference_data.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/summary_cluster.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/clusters.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/assembly_compare.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/vfdb_parser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/pubmlst_ref_preparer_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/mlst_reporter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/report.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/link.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/refdata_query.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/mlst_reporter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/report_filter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/cdhit.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/megares_zip_parser.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/mic_plotter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/ref_genes_getter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/megares_data_finder.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/ref_seq_chooser.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/summary_cluster_variant.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/summary_sample.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/summary.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/flag.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/version.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/summary.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/prepareref_tb.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/test.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/prepareref.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/summary.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/run.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/getref.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/refquery.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/flag.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/aln2meta.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/pubmlstspecies.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/expandflag.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/version.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/getref.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/prepareref.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/micplot.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/aln2meta.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/pubmlstget.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/prepareref_tb.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/reportfilter.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/pubmlstspecies.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/refquery.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/run.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__pycache__/flag.cpython-313.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/prepareref_tb.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/getref.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/expandflag.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/micplot.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/pubmlstget.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/refquery.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/aln2meta.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/flag.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/prepareref_tb.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/version.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/getref.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/reportfilter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/pubmlstspecies.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/summary.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/run.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/expandflag.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/reportfilter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/prepareref.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/micplot.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/pubmlstget.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/report_flag_expander.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/aln_to_metadata.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/samtools_variants.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks/run.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tb_data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data/panel.20190102.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tb_data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data/panel.20181221.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tb_data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data/panel.20190102.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tb_data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data/panel.20181221.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tb_data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data/panel.20181115.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tb_data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data/NC_000962.3.gb -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tb_data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data/panel.20190102.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tb_data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data/NC_000962.3.fa.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tb_data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data/panel.20181115.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tb_data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data/panel.20181115.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tb_data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/summary_sample.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/cdhit.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/megares_data_finder.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data/NC_000962.3.gb -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tb_data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data/panel.20190102.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tb_data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/report_filter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/samtools_variants.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/aln_to_metadata.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/sequence_metadata.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/external_progs.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/cluster.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/ref_genes_getter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/bam_parse.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/mic_plotter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/vfdb_parser.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/read_store.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/sequence_variant.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/assembly_variants.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/pubmlst_ref_preparer.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/faidx.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/versions.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/pubmlst_getter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/report.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/scaffold_graph.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/read_filter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/histogram.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/ref_seq_chooser.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/summary_cluster_variant.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/card_record.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/sequence_metadata.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/assembly.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/ref_preparer.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/external_progs.py to external_progs.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/megares_zip_parser.py to megares_zip_parser.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/flag.py to flag.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/mapping.py to mapping.cpython-313.pyc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/vcfcall_ariba.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/fermilite_ariba.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/report_flag_expander.py to report_flag_expander.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/reference_data.py to reference_data.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/mlst_profile.py to mlst_profile.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/card_record.py to card_record.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/ref_preparer.py to ref_preparer.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/sequence_variant.py to sequence_variant.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/read_store.py to read_store.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/common.py to common.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/ref_genes_getter_test.py to ref_genes_getter_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/histogram_test.py to histogram_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/test_refdata_query.py to test_refdata_query.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/read_filter.py to read_filter.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/bam_parse.py to bam_parse.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/assembly.py to assembly.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/histogram.py to histogram.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/pubmlst_ref_preparer.py to pubmlst_ref_preparer.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/flag.py to flag.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/scaffold_graph.py to scaffold_graph.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/assembly_compare.py to assembly_compare.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/faidx.py to faidx.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/mapping.py to mapping.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/vfdb_parser.py to vfdb_parser.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__init__.py to __init__.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/clusters.py to clusters.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/assembly_variants.py to assembly_variants.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/summary_cluster.py to summary_cluster.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/summary_sample_test.py to summary_sample_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/tb_test.py to tb_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/mlst_reporter_test.py to mlst_reporter_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/mlst_profile_test.py to mlst_profile_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/megares_zip_parser_test.py to megares_zip_parser_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/summary_cluster_test.py to summary_cluster_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/card_record_test.py to card_record_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/versions_test.py to versions_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/clusters_test.py to clusters_test.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/read_store_test.py to read_store_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/link_test.py to link_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/mic_plotter_test.py to mic_plotter_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/reference_data_test.py to reference_data_test.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/scaffold_graph_test.py to scaffold_graph_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/summary_cluster_test.py to summary_cluster_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/histogram_test.py to histogram_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/report_flag_expander_test.py to report_flag_expander_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/summary_cluster_variant_test.py to summary_cluster_variant_test.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/aln_to_metadata_test.py to aln_to_metadata_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/megares_zip_parser_test.py to megares_zip_parser_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/bam_parse_test.py to bam_parse_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/flag_test.py to flag_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/megares_data_finder_test.py to megares_data_finder_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/pubmlst_getter_test.py to pubmlst_getter_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/samtools_variants_test.py to samtools_variants_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/clusters_test.py to clusters_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/vfdb_parser_test.py to vfdb_parser_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/cluster_test.py to cluster_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/assembly_compare_test.py to assembly_compare_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/versions_test.py to versions_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/summary_test.py to summary_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/read_filter_test.py to read_filter_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/report_filter_test.py to report_filter_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/external_progs_test.py to external_progs_test.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/ref_preparer_test.py to ref_preparer_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/cdhit_test.py to cdhit_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/tb_test.py to tb_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/common_test.py to common_test.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/__init__.py to __init__.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/external_progs_test.py to external_progs_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/samtools_variants_test.py to samtools_variants_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/link_test.py to link_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/pubmlst_getter_test.py to pubmlst_getter_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/assembly_compare_test.py to assembly_compare_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/flag_test.py to flag_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/cluster_test.py to cluster_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/assembly_variants_test.py to assembly_variants_test.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/assembly_test.py to assembly_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/faidx_test.py to faidx_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/summary_test.py to summary_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/read_filter_test.py to read_filter_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/pubmlst_ref_preparer_test.py to pubmlst_ref_preparer_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/sequence_metadata_test.py to sequence_metadata_test.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/mapping_test.py to mapping_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/mlst_profile_test.py to mlst_profile_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/sequence_variant_test.py to sequence_variant_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/test_refdata_query.py to test_refdata_query.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/megares_data_finder_test.py to megares_data_finder_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/mic_plotter_test.py to mic_plotter_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/sequence_metadata_test.py to sequence_metadata_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/faidx_test.py to faidx_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/ref_genes_getter_test.py to ref_genes_getter_test.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/ncbi_getter_test.py to ncbi_getter_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/assembly_variants_test.py to assembly_variants_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/summary_cluster_variant_test.py to summary_cluster_variant_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/common_test.py to common_test.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/ref_seq_chooser_test.py to ref_seq_chooser_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/report_flag_expander_test.py to report_flag_expander_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/mlst_reporter_test.py to mlst_reporter_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/card_record_test.py to card_record_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/report_filter_test.py to report_filter_test.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/versions.py to versions.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/reference_data.py to reference_data.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/summary_cluster.py to summary_cluster.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/clusters.py to clusters.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/assembly_compare.py to assembly_compare.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/bam_parse_test.py to bam_parse_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/cdhit_test.py to cdhit_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/reference_data_test.py to reference_data_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/sequence_variant_test.py to sequence_variant_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/vfdb_parser_test.py to vfdb_parser_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tests/pubmlst_ref_preparer_test.py to pubmlst_ref_preparer_test.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/mlst_reporter.py to mlst_reporter.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/report.py to report.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/link.py to link.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/refdata_query.py to refdata_query.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/mlst_reporter.py to mlst_reporter.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/report_filter.py to report_filter.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/cdhit.py to cdhit.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/megares_zip_parser.py to megares_zip_parser.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/mic_plotter.py to mic_plotter.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/ref_genes_getter.py to ref_genes_getter.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/megares_data_finder.py to megares_data_finder.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/ref_seq_chooser.py to ref_seq_chooser.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/summary_cluster_variant.py to summary_cluster_variant.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/summary_sample.py to summary_sample.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/summary.py to summary.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/expandflag.py to expandflag.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/micplot.py to micplot.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/pubmlstget.py to pubmlstget.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/refquery.py to refquery.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/aln2meta.py to aln2meta.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/flag.py to flag.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/version.py to version.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/prepareref_tb.py to prepareref_tb.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/version.py to version.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__init__.py to __init__.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/getref.py to getref.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/refquery.py to refquery.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/aln2meta.py to aln2meta.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/reportfilter.py to reportfilter.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/test.py to test.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/pubmlstspecies.py to pubmlstspecies.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/summary.py to summary.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/run.py to run.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/__init__.py to __init__.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/expandflag.py to expandflag.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/reportfilter.py to reportfilter.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/prepareref.py to prepareref.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/micplot.py to micplot.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/pubmlstget.py to pubmlstget.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/report_flag_expander.py to report_flag_expander.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/aln_to_metadata.py to aln_to_metadata.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tasks/run.py to run.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tb.py to tb.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/report_filter.py to report_filter.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/samtools_variants.py to samtools_variants.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/summary_sample.py to summary_sample.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/cdhit.py to cdhit.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/megares_data_finder.py to megares_data_finder.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/aln_to_metadata.py to aln_to_metadata.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/sequence_metadata.py to sequence_metadata.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/external_progs.py to external_progs.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/cluster.py to cluster.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/ref_genes_getter.py to ref_genes_getter.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/bam_parse.py to bam_parse.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/__init__.py to __init__.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/mic_plotter.py to mic_plotter.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/vfdb_parser.py to vfdb_parser.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/read_store.py to read_store.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/sequence_variant.py to sequence_variant.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/assembly_variants.py to assembly_variants.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/pubmlst_ref_preparer.py to pubmlst_ref_preparer.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/faidx.py to faidx.cpython-313.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/versions.py to versions.cpython-313.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/pubmlst_getter.py to pubmlst_getter.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/report.py to report.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/scaffold_graph.py to scaffold_graph.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/read_filter.py to read_filter.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/histogram.py to histogram.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/tb.py to tb.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/ref_seq_chooser.py to ref_seq_chooser.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/summary_cluster_variant.py to summary_cluster_variant.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/card_record.py to card_record.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/sequence_metadata.py to sequence_metadata.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/assembly.py to assembly.cpython-313.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.13/dist-packages/ariba/ref_preparer.py to ref_preparer.cpython-313.pyc
 running install_egg_info
 running egg_info
 creating ariba.egg-info
@@ -4301,1009 +4337,1009 @@
 running build_scripts
 running install_lib
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/fermilite_ariba.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/minimap_ariba.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/vcfcall_ariba.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/external_progs.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/megares_zip_parser.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/flag.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/mapping.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/report_flag_expander.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/reference_data.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/mlst_profile.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/card_record.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/ref_preparer.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/sequence_variant.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/clusters.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/ref_genes_getter.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/read_filter.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/aln_to_metadata.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/histogram.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/mlst_profile.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/reference_data.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/flag.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/summary_cluster_variant.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/link.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/bam_parse.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/read_store.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/samtools_variants.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/summary_sample.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/mlst_reporter.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/pubmlst_ref_preparer.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/tb.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/report_filter.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/vfdb_parser.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/report_flag_expander.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/megares_data_finder.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/summary_cluster.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/assembly_compare.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/external_progs.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/versions.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/cdhit.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/ref_seq_chooser.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/pubmlst_getter.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/summary.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/mic_plotter.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/report.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/sequence_metadata.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/scaffold_graph.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/common.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/assembly.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/cluster.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/refdata_query.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/card_record.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/sequence_variant.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/mapping.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/faidx.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/ref_preparer.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/megares_zip_parser.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/assembly_variants.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/read_store.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/common.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/read_filter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/bam_parse.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/test_run_data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/test_run_data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/test_run_data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data/metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/test_run_data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/test_run_data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/test_run_data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/test_run_data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data/ref_seqs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/test_run_data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/mlst_profile.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/common.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/test_run_data/metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/test_run_data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/assembly.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/histogram.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/pubmlst_ref_preparer.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/flag.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/scaffold_graph.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/assembly_compare.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/faidx.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/mapping.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/vfdb_parser.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/clusters.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/assembly_variants.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/summary_cluster.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/ref_genes_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/histogram_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/test_refdata_query.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/summary_sample_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/read_store_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/link_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/mic_plotter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/reference_data_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/scaffold_graph_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/summary_cluster_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/aln_to_metadata_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/tb_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/mlst_reporter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/mlst_profile_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/assembly_variants_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/ref_genes_getter_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/bam_parse_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/link_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/tb_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/read_store_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/flag_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/assembly_compare_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/common_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/sequence_metadata_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/samtools_variants_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/megares_zip_parser_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/summary_sample_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/card_record_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/pubmlst_getter_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/mlst_reporter_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/mapping_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/report_flag_expander_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/summary_cluster_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/assembly_variants_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/summary_cluster_variant_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/cdhit_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/mic_plotter_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/summary_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/sequence_variant_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/pubmlst_getter_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/cluster_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/faidx_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/assembly_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/ncbi_getter_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/mic_plotter_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/scaffold_graph_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/reference_data_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/read_filter_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/tb_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/histogram_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/bam_parse_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/vfdb_parser_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/reference_data_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/scaffold_graph_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/read_store_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/summary_sample_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/mlst_profile_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/versions_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/megares_data_finder_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/summary_cluster_variant_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/sequence_metadata_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/ref_seq_chooser_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/external_progs_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/histogram_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/mapping_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/test_refdata_query.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/sequence_variant_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/pubmlst_ref_preparer_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/clusters_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/link_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/aln_to_metadata_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/common_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/report_filter_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/mlst_profile_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/report_flag_expander_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/versions_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/summary_cluster_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/ref_preparer_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/report_filter_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/ref_genes_getter_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/ncbi_getter_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/card_record_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/megares_zip_parser_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/flag_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/pubmlst_ref_preparer_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/ref_seq_chooser_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/assembly_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/assembly_compare_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/clusters_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/mlst_reporter_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__pycache__/faidx_test.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/megares_zip_parser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/summary_cluster_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/card_record_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/versions_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/clusters_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/read_store_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/scaffold_graph_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/histogram_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/report_flag_expander_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/summary_cluster_variant_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/aln_to_metadata_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/summary_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/read_filter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/report_filter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/external_progs_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/ref_preparer_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/samtools_variants_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/link_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/pubmlst_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/assembly_compare_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/flag_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/cluster_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/assembly_variants_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/assembly_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/mapping_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/test_refdata_query.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/megares_data_finder_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/mic_plotter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/sequence_metadata_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/faidx_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/ref_genes_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_fasta_file.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads.no_link_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/test_common_cat_files.in.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_rename_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_test_init.fofn -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_check_spades_log_file.log.bad -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/graph_test_update_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/megares_zip_parser_write_files
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/megares_zip_parser_write_files
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/megares_zip_parser_write_files
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/megares_zip_parser_write_files
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_count_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.in.3.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.in.4.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_check_not_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_test_run.in.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_init_fails.empty.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_profile_test.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_test_whole_run.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_check_too_long.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.vcf -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_cat_genes_match_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.rename_info -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/vfdb_parser_test_run.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_fix_out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_run_fermilite.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_write_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/graph_test_update_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_refdata.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_rename_sequences.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_rename_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/report_filter_test_init_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_test_whole_run.out.csv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_count_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_init_fails.empty.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_init_ok.rename.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_init_ok.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_run_fermilite.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_sequence.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_init_ok.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/report_filter_test_init_bad.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads.make_link_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_fix_out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/tb_genbank_to_gene_coords.gb -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads.no_link_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_parse.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_fix_out.rename -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_init_ok.params.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_sequence.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_sequence.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/test_common_cat_files.in.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/report_filter_test_load_report_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/dummy.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.cluster -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_bowtie2_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parse_extract_files_ok.zip -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/pubmlst_rename_seqs.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.profile.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/00.rename_info -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/refdata_query_prepareref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_sample_test_load_file.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_dummy_db.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_init_fails.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_parse.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads.no_link_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_to_matrix.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/vfdb_parser_test_run.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_fix_in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.cluster -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_load_annotations.csv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_init_ok.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_sort_file.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_bowtie2_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_profile_test.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_bowtie2_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_rename_sequences.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads.make_link.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_init_ok.params.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_test_load_fofn -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parse_extract_files_ok.zip -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_get_reads.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/report_filter_test_run.expected.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads.no_link.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_sequence_type.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.in.1.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/test_common_cat_files.in.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/report_filter_test_init_bad.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_dummy_db.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_remove_bad_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/graph_test_update_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_parse.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_load_summary_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_test_write_distance_matrix.distances -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_fake_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/tb_report_to_resistance_dict.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.in.3.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/report_flag_expander.run.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads.make_link_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_test_run.in.read_store -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/report_flag_expander.run.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_parse.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_bowtie2_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_dummy_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_sample_test_var_groups.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/test_common_cat_files.in.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_to_matrix.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.in.2.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_profile_test.init.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_rename_sequences.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_sequence.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_cat_genes_match_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_dummy_db.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_rename_sequences.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_fix_in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_check_ok.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_test_run.in.read_store -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_profile_test.init.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_all_metadata_tsvs.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_parse.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/graph_test_write_all_links_to_file.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/pubmlst_getter.dbases.xml -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_check_too_short.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_test_write_distance_matrix.distances -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads.no_link.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_sequence_type.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_sample_test_var_groups.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.profile.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.smi -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_run_fermilite.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/report_filter_test_init_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_sam_to_fastq.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/report_filter_test_run.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/vfdb_parser_test_run.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2/genes.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/report_filter_test_load_report_bad.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_test_load_input_files.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_fix_out.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_run_fermilite.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_refdata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads.make_link_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_test_run.in.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/tb_report_to_resistance_dict.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_load_summary_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.vcf -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/graph_test_write_all_links_to_file.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_test_whole_run.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_check_not_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads.make_link_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_clean.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_fix_out.rename -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_test_load_input_files.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.ariba.report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/report_filter_test_write_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_sort_file.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_test_whole_run.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_test_init.fofn -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_sam_to_fastq.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_init_fails.empty.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/test_common_cat_files.in.3 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/report_flag_expander.run.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/tb_genbank_to_gene_coords.gb -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_test_load_input_files.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_sample_test_load_file.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_fix_out.removed.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_count_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_count_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_load_data_info_file -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run.out
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_fasta_file.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/report_flag_expander.run.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refdata_query_prepareref.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_test_load_fofn -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_dummy_db.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_init_fails.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_load_mic_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_bowtie2_unsorted.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/report_filter_test_run.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_all_fasta_files.in.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_get_reads.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_refdata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/vfdb_parser_test_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_to_matrix.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_check_ok.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/dummy.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/report_filter_test_load_report_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_sequence_type.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_sequence_type.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_compress_and_index_file.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads.no_link_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.in.4.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_remove_bad_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_sort_file.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_bowtie2_unsorted.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.params.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/clusters_run_with_tb.ref
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_all_fasta_files.in.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/report_filter_test_write_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/graph_test_update_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/report_filter_test_run.expected.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene2.tfa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/profile.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.in.2.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/test_common_cat_files.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.rename_info -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_init_ok.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/test_common_cat_files.in.3 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_clean.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_dummy_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_fix_out.removed.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_fake_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_compress_and_index_file.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/megares_zip_parser_write_files
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/megares_zip_parser_write_files
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/megares_zip_parser_write_files
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/megares_zip_parser_write_files
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/pubmlst_rename_seqs.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_load_data_info_file -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_dummy_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_init_ok.rename.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_check_too_short.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_init_refdata.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/pubmlst_getter.dbases.xml -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_sort_file.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_init_fails.empty.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_run_fermilite.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/link_test_init.reads.make_link.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_run_fermilite.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_preparer_test_run.in.1.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/test_common_cat_files.out -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_test_whole_run.out.csv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/refcheck_test_check_too_long.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_load_annotations.csv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_to_matrix.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/summary_test_load_input_files.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/ncbi_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/common_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/ref_seq_chooser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/bam_parse_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/flag_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/megares_data_finder_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/pubmlst_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/samtools_variants_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/clusters_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/vfdb_parser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/cluster_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/assembly_compare_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/versions_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/ref_preparer_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/cdhit_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/tb_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/common_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/external_progs_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/assembly_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/faidx_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/summary_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/read_filter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/pubmlst_ref_preparer_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/sequence_metadata_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/mapping_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/mlst_profile_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/reference_data_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/sequence_variant_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/ncbi_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/assembly_variants_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/summary_cluster_variant_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/ref_seq_chooser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/report_flag_expander_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/mlst_reporter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/card_record_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/report_filter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
-creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/pubmlst_getter.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/common.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/mapping.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/card_record.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/ref_seq_chooser.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/assembly.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/cluster.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/clusters.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/summary_sample.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/mlst_reporter.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/ref_preparer.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/scaffold_graph.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/report.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/cdhit.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/reference_data.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/flag.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/faidx.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/summary_cluster.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/read_filter.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/report_filter.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/megares_zip_parser.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/mic_plotter.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/versions.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/tb.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/summary_cluster_variant.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/bam_parse.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/ref_genes_getter.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/histogram.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/assembly_compare.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/pubmlst_ref_preparer.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/refdata_query.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/megares_data_finder.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/aln_to_metadata.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/link.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/assembly_variants.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/mlst_profile.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/vfdb_parser.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/external_progs.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/sequence_metadata.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/summary.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/samtools_variants.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/report_flag_expander.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/sequence_variant.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__pycache__/read_store.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/versions.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/reference_data.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/summary_cluster.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/clusters.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/assembly_compare.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/vfdb_parser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tests/pubmlst_ref_preparer_test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/mlst_reporter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/report.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/link.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/refdata_query.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/mlst_reporter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/report_filter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/cdhit.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/megares_zip_parser.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/mic_plotter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/ref_genes_getter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/megares_data_finder.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/ref_seq_chooser.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/summary_cluster_variant.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/summary_sample.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/summary.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/flag.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/version.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/run.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/pubmlstspecies.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/flag.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/pubmlstget.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/prepareref_tb.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/flag.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/version.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/expandflag.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/prepareref.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/aln2meta.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/refquery.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/test.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/micplot.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/run.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/summary.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/reportfilter.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/aln2meta.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/pubmlstget.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/test.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/pubmlstspecies.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/getref.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/prepareref.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/summary.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/expandflag.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__pycache__/micplot.cpython-312.pyc -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__pycache__
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/prepareref_tb.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/getref.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/expandflag.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/micplot.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/pubmlstget.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/refquery.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/aln2meta.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/flag.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/prepareref_tb.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/version.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/getref.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/reportfilter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/test.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/pubmlstspecies.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/summary.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/run.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/expandflag.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/reportfilter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/prepareref.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/micplot.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/pubmlstget.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/report_flag_expander.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/aln_to_metadata.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/samtools_variants.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tasks/run.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
 creating /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tb_data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data/panel.20190102.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tb_data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data/panel.20181221.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tb_data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data/panel.20190102.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tb_data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data/panel.20181221.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tb_data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data/panel.20181115.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tb_data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data/NC_000962.3.gb -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tb_data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data/panel.20190102.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tb_data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data/NC_000962.3.fa.gz -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tb_data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data/panel.20181115.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tb_data
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data/panel.20181115.txt -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tb_data
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/summary_sample.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/cdhit.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/megares_data_finder.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data/NC_000962.3.gb -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tb_data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb_data/panel.20190102.json -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tb_data
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/report_filter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/samtools_variants.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/aln_to_metadata.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/sequence_metadata.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/external_progs.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/cluster.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/ref_genes_getter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/bam_parse.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/mic_plotter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/vfdb_parser.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/read_store.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/sequence_variant.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/assembly_variants.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/pubmlst_ref_preparer.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/faidx.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/versions.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
 copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/pubmlst_getter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/report.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/scaffold_graph.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/read_filter.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/histogram.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/tb.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/ref_seq_chooser.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/summary_cluster_variant.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/card_record.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/sequence_metadata.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/assembly.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/ariba/ref_preparer.py -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/external_progs.py to external_progs.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/megares_zip_parser.py to megares_zip_parser.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/flag.py to flag.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/mapping.py to mapping.cpython-312.pyc
+copying /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.12_ariba/build/fermilite_ariba.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/report_flag_expander.py to report_flag_expander.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/reference_data.py to reference_data.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/mlst_profile.py to mlst_profile.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/card_record.py to card_record.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/ref_preparer.py to ref_preparer.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/sequence_variant.py to sequence_variant.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/read_store.py to read_store.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/common.py to common.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/ref_genes_getter_test.py to ref_genes_getter_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/histogram_test.py to histogram_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/test_refdata_query.py to test_refdata_query.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/read_filter.py to read_filter.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/bam_parse.py to bam_parse.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/assembly.py to assembly.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/histogram.py to histogram.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/pubmlst_ref_preparer.py to pubmlst_ref_preparer.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/flag.py to flag.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/scaffold_graph.py to scaffold_graph.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/assembly_compare.py to assembly_compare.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/faidx.py to faidx.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/mapping.py to mapping.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/vfdb_parser.py to vfdb_parser.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__init__.py to __init__.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/clusters.py to clusters.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/assembly_variants.py to assembly_variants.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/summary_cluster.py to summary_cluster.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/summary_sample_test.py to summary_sample_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/tb_test.py to tb_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/mlst_reporter_test.py to mlst_reporter_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/mlst_profile_test.py to mlst_profile_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/megares_zip_parser_test.py to megares_zip_parser_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/summary_cluster_test.py to summary_cluster_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/card_record_test.py to card_record_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/versions_test.py to versions_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/clusters_test.py to clusters_test.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/read_store_test.py to read_store_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/link_test.py to link_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/mic_plotter_test.py to mic_plotter_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/reference_data_test.py to reference_data_test.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/scaffold_graph_test.py to scaffold_graph_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/summary_cluster_test.py to summary_cluster_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/histogram_test.py to histogram_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/report_flag_expander_test.py to report_flag_expander_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/summary_cluster_variant_test.py to summary_cluster_variant_test.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/aln_to_metadata_test.py to aln_to_metadata_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/megares_zip_parser_test.py to megares_zip_parser_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/bam_parse_test.py to bam_parse_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/flag_test.py to flag_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/megares_data_finder_test.py to megares_data_finder_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/pubmlst_getter_test.py to pubmlst_getter_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/samtools_variants_test.py to samtools_variants_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/clusters_test.py to clusters_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/vfdb_parser_test.py to vfdb_parser_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/cluster_test.py to cluster_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/assembly_compare_test.py to assembly_compare_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/versions_test.py to versions_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/summary_test.py to summary_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/read_filter_test.py to read_filter_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/report_filter_test.py to report_filter_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/external_progs_test.py to external_progs_test.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/ref_preparer_test.py to ref_preparer_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/cdhit_test.py to cdhit_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/tb_test.py to tb_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/common_test.py to common_test.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/__init__.py to __init__.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/external_progs_test.py to external_progs_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/samtools_variants_test.py to samtools_variants_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/link_test.py to link_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/pubmlst_getter_test.py to pubmlst_getter_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/assembly_compare_test.py to assembly_compare_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/flag_test.py to flag_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/cluster_test.py to cluster_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/assembly_variants_test.py to assembly_variants_test.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/assembly_test.py to assembly_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/faidx_test.py to faidx_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/summary_test.py to summary_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/read_filter_test.py to read_filter_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/pubmlst_ref_preparer_test.py to pubmlst_ref_preparer_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/sequence_metadata_test.py to sequence_metadata_test.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/mapping_test.py to mapping_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/mlst_profile_test.py to mlst_profile_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/sequence_variant_test.py to sequence_variant_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/test_refdata_query.py to test_refdata_query.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/megares_data_finder_test.py to megares_data_finder_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/mic_plotter_test.py to mic_plotter_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/sequence_metadata_test.py to sequence_metadata_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/faidx_test.py to faidx_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/ref_genes_getter_test.py to ref_genes_getter_test.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/ncbi_getter_test.py to ncbi_getter_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/assembly_variants_test.py to assembly_variants_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/summary_cluster_variant_test.py to summary_cluster_variant_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/common_test.py to common_test.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/ref_seq_chooser_test.py to ref_seq_chooser_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/report_flag_expander_test.py to report_flag_expander_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/mlst_reporter_test.py to mlst_reporter_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/card_record_test.py to card_record_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/report_filter_test.py to report_filter_test.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/versions.py to versions.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/reference_data.py to reference_data.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/summary_cluster.py to summary_cluster.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/clusters.py to clusters.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/assembly_compare.py to assembly_compare.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/bam_parse_test.py to bam_parse_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/cdhit_test.py to cdhit_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/reference_data_test.py to reference_data_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/sequence_variant_test.py to sequence_variant_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/vfdb_parser_test.py to vfdb_parser_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tests/pubmlst_ref_preparer_test.py to pubmlst_ref_preparer_test.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/mlst_reporter.py to mlst_reporter.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/report.py to report.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/link.py to link.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/refdata_query.py to refdata_query.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/mlst_reporter.py to mlst_reporter.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/report_filter.py to report_filter.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/cdhit.py to cdhit.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/megares_zip_parser.py to megares_zip_parser.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/mic_plotter.py to mic_plotter.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/ref_genes_getter.py to ref_genes_getter.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/megares_data_finder.py to megares_data_finder.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/ref_seq_chooser.py to ref_seq_chooser.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/summary_cluster_variant.py to summary_cluster_variant.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/summary_sample.py to summary_sample.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/summary.py to summary.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/expandflag.py to expandflag.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/micplot.py to micplot.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/pubmlstget.py to pubmlstget.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/refquery.py to refquery.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/aln2meta.py to aln2meta.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/flag.py to flag.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/version.py to version.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/prepareref_tb.py to prepareref_tb.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/version.py to version.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__init__.py to __init__.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/getref.py to getref.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/refquery.py to refquery.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/aln2meta.py to aln2meta.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/reportfilter.py to reportfilter.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/test.py to test.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/pubmlstspecies.py to pubmlstspecies.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/summary.py to summary.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/run.py to run.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/__init__.py to __init__.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/expandflag.py to expandflag.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/reportfilter.py to reportfilter.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/prepareref.py to prepareref.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/micplot.py to micplot.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/pubmlstget.py to pubmlstget.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/report_flag_expander.py to report_flag_expander.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/aln_to_metadata.py to aln_to_metadata.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tasks/run.py to run.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tb.py to tb.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/report_filter.py to report_filter.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/samtools_variants.py to samtools_variants.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/summary_sample.py to summary_sample.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/cdhit.py to cdhit.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/megares_data_finder.py to megares_data_finder.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/aln_to_metadata.py to aln_to_metadata.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/sequence_metadata.py to sequence_metadata.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/external_progs.py to external_progs.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/cluster.py to cluster.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/ref_genes_getter.py to ref_genes_getter.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/bam_parse.py to bam_parse.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/__init__.py to __init__.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/mic_plotter.py to mic_plotter.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/vfdb_parser.py to vfdb_parser.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/read_store.py to read_store.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/sequence_variant.py to sequence_variant.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/assembly_variants.py to assembly_variants.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/pubmlst_ref_preparer.py to pubmlst_ref_preparer.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/faidx.py to faidx.cpython-312.pyc
+byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/versions.py to versions.cpython-312.pyc
 byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/pubmlst_getter.py to pubmlst_getter.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/report.py to report.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/scaffold_graph.py to scaffold_graph.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/read_filter.py to read_filter.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/histogram.py to histogram.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/tb.py to tb.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/ref_seq_chooser.py to ref_seq_chooser.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/summary_cluster_variant.py to summary_cluster_variant.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/card_record.py to card_record.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/sequence_metadata.py to sequence_metadata.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/assembly.py to assembly.cpython-312.pyc
-byte-compiling /build/reproducible-path/ariba-2.14.7+ds/debian/ariba/usr/lib/python3.12/dist-packages/ariba/ref_preparer.py to ref_preparer.cpython-312.pyc
 running install_egg_info
 running egg_info
 writing ariba.egg-info/PKG-INFO
@@ -5345,8 +5381,8 @@
    dh_gencontrol -O--buildsystem=pybuild
    dh_md5sums -O--buildsystem=pybuild
    dh_builddeb -O--buildsystem=pybuild
-dpkg-deb: building package 'ariba' in '../ariba_2.14.7+ds-5_amd64.deb'.
 dpkg-deb: building package 'ariba-dbgsym' in '../ariba-dbgsym_2.14.7+ds-5_amd64.deb'.
+dpkg-deb: building package 'ariba' in '../ariba_2.14.7+ds-5_amd64.deb'.
  dpkg-genbuildinfo --build=binary -O../ariba_2.14.7+ds-5_amd64.buildinfo
  dpkg-genchanges --build=binary -O../ariba_2.14.7+ds-5_amd64.changes
 dpkg-genchanges: info: binary-only upload (no source code included)
@@ -5354,12 +5390,14 @@
 dpkg-buildpackage: info: binary-only upload (no source included)
 dpkg-genchanges: info: not including original source code in upload
 I: copying local configuration
+I: user script /srv/workspace/pbuilder/712969/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/712969/tmp/hooks/B01_cleanup finished
 I: unmounting dev/ptmx filesystem
 I: unmounting dev/pts filesystem
 I: unmounting dev/shm filesystem
 I: unmounting proc filesystem
 I: unmounting sys filesystem
 I: cleaning the build env 
-I: removing directory /srv/workspace/pbuilder/2982031 and its subdirectories
-I: Current time: Sun Jan 11 06:41:26 -12 2026
-I: pbuilder-time-stamp: 1768156886
+I: removing directory /srv/workspace/pbuilder/712969 and its subdirectories
+I: Current time: Tue Dec 10 02:45:11 +14 2024
+I: pbuilder-time-stamp: 1733748311