I: pbuilder: network access will be disabled during build I: Current time: Wed May 3 10:40:54 -12 2023 I: pbuilder-time-stamp: 1683153654 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [ariba_2.14.6+ds-5.dsc] I: copying [./ariba_2.14.6+ds.orig.tar.xz] I: copying [./ariba_2.14.6+ds-5.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Jan 7 02:59:17 2023 -12 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./ariba_2.14.6+ds-5.dsc: no acceptable signature found dpkg-source: info: extracting ariba in ariba-2.14.6+ds dpkg-source: info: unpacking ariba_2.14.6+ds.orig.tar.xz dpkg-source: info: unpacking ariba_2.14.6+ds-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs_for_extension.patch dpkg-source: info: applying use_bwa_compatible_fermi-lite.patch dpkg-source: info: applying add-testdata.patch dpkg-source: info: applying disable-tests-with-internet-access.patch dpkg-source: info: applying support-pymummer-0.11.patch dpkg-source: info: applying run-debian-spades-wrapper.patch dpkg-source: info: applying port-to-pytest.patch dpkg-source: info: applying mpileup-1.16.patch dpkg-source: info: applying skip-cluster-test.patch dpkg-source: info: applying adjust-bowtie2-test.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2494563/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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=15' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='44508c85d3f044c0b13dc37b693b642a' 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='2494563' PS1='# ' PS2='> ' 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.n66mAJHt/pbuilderrc_bmYt --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.n66mAJHt/b1 --logfile b1/build.log ariba_2.14.6+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://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 09:23 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar -rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/2494563/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3-biopython, python3-all-dev, python3-dendropy, python3-setuptools, python3-pymummer, python3-pysam, python3-pytest, python3-bs4, python3-matplotlib, python3-tk, bowtie2, cd-hit, mash, libminimap-dev, libfml-dev, mummer, fastaq, help2man, asciidoctor, spades dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-dendropy; however: Package python3-dendropy is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pymummer; however: Package python3-pymummer is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-bs4; however: Package python3-bs4 is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-tk; however: Package python3-tk is not installed. pbuilder-satisfydepends-dummy depends on bowtie2; however: Package bowtie2 is not installed. pbuilder-satisfydepends-dummy depends on cd-hit; however: Package cd-hit is not installed. pbuilder-satisfydepends-dummy depends on mash; however: Package mash is not installed. pbuilder-satisfydepends-dummy depends on libminimap-dev; however: Package libminimap-dev is not installed. pbuilder-satisfydepends-dummy depends on libfml-dev; however: Package libfml-dev is not installed. pbuilder-satisfydepends-dummy depends on mummer; however: Package mummer is not installed. pbuilder-satisfydepends-dummy depends on fastaq; however: Package fastaq is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor is not installed. pbuilder-satisfydepends-dummy depends on spades; however: Package spades is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bamtools{a} blt{a} bowtie2{a} bsdextrautils{a} bwa{a} ca-certificates{a} cd-hit{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fastaq{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-lyx{a} fonts-urw-base35{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbamtools2.5.2{a} libblas3{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libcapnp-0.9.2{a} libcurl3-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfml-dev{a} libfml0{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libgsl27{a} libgslcblas0{a} libharfbuzz0b{a} libhts3{a} libhtscodecs2{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp25{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libminimap-dev{a} libminimap0{a} libmurmurhash2{a} libncurses6{a} libnghttp2-14{a} libnlopt0{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libopenjp2-7{a} libpipeline1{a} libpng16-16{a} libproc2-0{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8{a} librtmp1{a} libruby{a} libruby3.1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssw0{a} libsub-override-perl{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxsimd-dev{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} m4{a} mailcap{a} man-db{a} mash{a} media-types{a} mime-support{a} mummer{a} openssl{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-all-dev{a} python3-appdirs{a} python3-attr{a} python3-beniget{a} python3-biopython{a} python3-brotli{a} python3-bs4{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dendropy{a} python3-dev{a} python3-distutils{a} python3-fonttools{a} python3-fs{a} python3-gast{a} python3-iniconfig{a} python3-joblib{a} python3-kiwisolver{a} python3-lib2to3{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-numpy{a} python3-packaging{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-pluggy{a} python3-ply{a} python3-py{a} python3-pymummer{a} python3-pyparsing{a} python3-pysam{a} python3-pytest{a} python3-pythran{a} python3-renderpm{a} python3-reportlab{a} python3-reportlab-accel{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-soupsieve{a} python3-sympy{a} python3-tk{a} python3-tz{a} python3-ufolib2{a} python3-yaml{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} rake{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} samtools{a} sensible-utils{a} sgml-base{a} spades{a} tk8.6-blt2.5{a} unicode-data{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-lato isympy-common javascript-common libarchive-cpio-perl libglib2.0-data libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-chardet python3-html5lib python3-olefile python3-psutil python3-pygments python3-simplejson shared-mime-info wget xdg-user-dirs zip 0 packages upgraded, 222 newly installed, 0 to remove and 0 not upgraded. Need to get 164 MB of archives. After unpacking 801 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libsigsegv2 amd64 2.14-1 [37.2 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 gawk amd64 1:5.2.1-2 [673 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 mailcap all 3.70+nmu1 [32.0 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 mime-support all 3.66 [10.9 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 16 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.8-1 [1407 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 rubygems-integration all 1.18 [6704 B] Get: 33 http://deb.debian.org/debian bookworm/main amd64 rake all 13.0.6-3 [83.9 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libruby amd64 1:3.1 [4972 B] Get: 38 http://deb.debian.org/debian bookworm/main amd64 ruby-sdbm amd64 1.0.0-5+b1 [15.4 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-2 [103 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libruby3.1 amd64 3.1.2-7 [5401 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 ruby3.1 amd64 3.1.2-7 [663 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 ruby-rubygems all 3.3.15-2 [293 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 ruby amd64 1:3.1 [5868 B] Get: 47 http://deb.debian.org/debian bookworm/main amd64 ruby-asciidoctor all 2.0.18-2 [211 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 asciidoctor all 2.0.18-2 [86.6 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-4 [149 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libjsoncpp25 amd64 1.9.5-4 [78.6 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 bamtools amd64 2.5.2+dfsg-4 [193 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libfontenc1 amd64 1:1.1.4-1 [24.3 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 fonts-urw-base35 all 20200910-7 [10.8 MB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4.1 [593 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 blt amd64 2.5.3+dfsg-4.1 [14.9 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 bowtie2 amd64 2.5.0-3+b2 [1409 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 bwa amd64 0.7.17-7+b2 [212 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 cd-hit amd64 4.8.1-4 [522 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-2 [131 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-9 [381 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.16.1-1 [607 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 fastaq all 3.17.0-5 [48.2 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 fonts-lyx all 2.3.7-1 [186 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 help2man amd64 1.49.3 [198 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-20 [9510 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 121 http://deb.debian.org/debian bookworm/main amd64 libcapnp-0.9.2 amd64 0.9.2-2 [1305 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libfml0 amd64 0.1+git20190320.b499514-1+b1 [71.4 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 libfml-dev amd64 0.1+git20190320.b499514-1+b1 [82.9 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 libgslcblas0 amd64 2.7.1+dfsg-3+b1 [116 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 libgsl27 amd64 2.7.1+dfsg-3+b1 [948 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB] Get: 141 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 142 http://deb.debian.org/debian bookworm/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1 [28.9 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 144 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 145 http://deb.debian.org/debian bookworm/main amd64 libminimap0 amd64 0.2-7 [21.8 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 libminimap-dev amd64 0.2-7 [32.6 kB] Get: 147 http://deb.debian.org/debian bookworm/main amd64 libmurmurhash2 amd64 1.5-3 [5860 B] Get: 148 http://deb.debian.org/debian bookworm/main amd64 libnlopt0 amd64 2.7.1-4+b4 [174 kB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 libopenblas0 amd64 0.3.21+ds-4 [32.6 kB] Get: 150 http://deb.debian.org/debian bookworm/main amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [4971 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 libopenblas-dev amd64 0.3.21+ds-4 [44.9 kB] Get: 152 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-1+b1 [189 kB] Get: 153 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6 [1988 kB] Get: 154 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6 [4738 kB] Get: 155 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B] Get: 156 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B] Get: 157 http://deb.debian.org/debian bookworm/main amd64 libqhull-r8.0 amd64 2020.2-5 [248 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB] Get: 159 http://deb.debian.org/debian bookworm/main amd64 libssw0 amd64 1.1-13 [19.7 kB] Get: 160 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.1 [285 kB] Get: 161 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-5 [316 kB] Get: 162 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.1 [99.2 kB] Get: 163 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.1 [109 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 libxsimd-dev amd64 8.1.0-7 [88.8 kB] Get: 165 http://deb.debian.org/debian bookworm/main amd64 libxslt1.1 amd64 1.1.35-1 [242 kB] Get: 166 http://deb.debian.org/debian bookworm/main amd64 mash amd64 2.3+dfsg-3+b1 [188 kB] Get: 167 http://deb.debian.org/debian bookworm/main amd64 mummer amd64 3.23+dfsg-8 [662 kB] Get: 168 http://deb.debian.org/debian bookworm/main amd64 python-matplotlib-data all 3.6.3-1 [2744 kB] Get: 169 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get: 170 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6 [615 kB] Get: 171 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB] Get: 172 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B] Get: 173 http://deb.debian.org/debian bookworm/main amd64 python3-appdirs all 1.4.4-3 [13.0 kB] Get: 174 http://deb.debian.org/debian bookworm/main amd64 python3-attr all 22.2.0-1 [65.4 kB] Get: 175 http://deb.debian.org/debian bookworm/main amd64 python3-gast all 0.5.2-2 [9364 B] Get: 176 http://deb.debian.org/debian bookworm/main amd64 python3-beniget all 0.4.1-3 [9920 B] Get: 177 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get: 178 http://deb.debian.org/debian bookworm/main amd64 python3-renderpm amd64 3.6.12-1+b1 [79.2 kB] Get: 179 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab-accel amd64 3.6.12-1+b1 [38.6 kB] Get: 180 http://deb.debian.org/debian bookworm/main amd64 python3-tk amd64 3.11.2-2 [98.2 kB] Get: 181 http://deb.debian.org/debian bookworm/main amd64 python3-pil.imagetk amd64 9.4.0-1.1+b1 [74.4 kB] Get: 182 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+b1 [472 kB] Get: 183 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab all 3.6.12-1 [564 kB] Get: 184 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 185 http://deb.debian.org/debian bookworm/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 186 http://deb.debian.org/debian bookworm/main amd64 python3-biopython amd64 1.80+dfsg-4+b1 [1593 kB] Get: 187 http://deb.debian.org/debian bookworm/main amd64 python3-brotli amd64 1.0.9-2+b6 [281 kB] Get: 188 http://deb.debian.org/debian bookworm/main amd64 python3-soupsieve all 2.3.2-1 [38.8 kB] Get: 189 http://deb.debian.org/debian bookworm/main amd64 python3-bs4 all 4.11.2-2 [121 kB] Get: 190 http://deb.debian.org/debian bookworm/main amd64 python3-contourpy amd64 1.0.7-1+b1 [176 kB] Get: 191 http://deb.debian.org/debian bookworm/main amd64 python3-cycler all 0.11.0-1 [8020 B] Get: 192 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get: 193 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB] Get: 194 http://deb.debian.org/debian bookworm/main amd64 python3-decorator all 5.1.1-3 [14.9 kB] Get: 195 http://deb.debian.org/debian bookworm/main amd64 python3-dendropy all 4.5.2-1 [275 kB] Get: 196 http://deb.debian.org/debian bookworm/main amd64 python3-ply all 3.11-5 [65.8 kB] Get: 197 http://deb.debian.org/debian bookworm/main amd64 python3-pythran amd64 0.11.0+ds-7 [427 kB] Get: 198 http://deb.debian.org/debian bookworm/main amd64 python3-scipy amd64 1.10.1-2 [15.2 MB] Get: 199 http://deb.debian.org/debian bookworm/main amd64 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB] Get: 200 http://deb.debian.org/debian bookworm/main amd64 python3-mpmath all 1.2.1-2 [418 kB] Get: 201 http://deb.debian.org/debian bookworm/main amd64 python3-sympy all 1.11.1-1 [4358 kB] Get: 202 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-3 [30.1 kB] Get: 203 http://deb.debian.org/debian bookworm/main amd64 python3-fs all 2.4.16-2 [95.2 kB] Get: 204 http://deb.debian.org/debian bookworm/main amd64 python3-lxml amd64 4.9.2-1+b1 [1194 kB] Get: 205 http://deb.debian.org/debian bookworm/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b2 [25.0 kB] Get: 206 http://deb.debian.org/debian bookworm/main amd64 unicode-data all 15.0.0-1 [7984 kB] Get: 207 http://deb.debian.org/debian bookworm/main amd64 python3-fonttools amd64 4.38.0-1+b1 [1012 kB] Get: 208 http://deb.debian.org/debian bookworm/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 209 http://deb.debian.org/debian bookworm/main amd64 python3-joblib all 1.2.0-4 [211 kB] Get: 210 http://deb.debian.org/debian bookworm/main amd64 python3-kiwisolver amd64 1.4.4-1+b1 [60.1 kB] Get: 211 http://deb.debian.org/debian bookworm/main amd64 python3-pyparsing all 3.0.9-1 [138 kB] Get: 212 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get: 213 http://deb.debian.org/debian bookworm/main amd64 python3-matplotlib amd64 3.6.3-1+b1 [6921 kB] Get: 214 http://deb.debian.org/debian bookworm/main amd64 python3-more-itertools all 8.10.0-2 [53.0 kB] Get: 215 http://deb.debian.org/debian bookworm/main amd64 python3-pluggy all 1.0.0+repack-1 [19.7 kB] Get: 216 http://deb.debian.org/debian bookworm/main amd64 python3-py all 1.11.0-1 [89.2 kB] Get: 217 http://deb.debian.org/debian bookworm/main amd64 python3-pymummer all 0.11.0-3 [11.4 kB] Get: 218 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB] Get: 219 http://deb.debian.org/debian bookworm/main amd64 python3-pytest all 7.2.1-2 [236 kB] Get: 220 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB] Get: 221 http://deb.debian.org/debian bookworm/main amd64 python3-yaml amd64 6.0-3+b2 [119 kB] Get: 222 http://deb.debian.org/debian bookworm/main amd64 spades amd64 3.15.5+dfsg-2 [8663 kB] Fetched 164 MB in 6s (25.4 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 ... 19596 files and directories currently installed.) Preparing to unpack .../readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../libsigsegv2_2.14-1_amd64.deb ... 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Unpacking python3-yaml (6.0-3+b2) ... Selecting previously unselected package spades. Preparing to unpack .../206-spades_3.15.5+dfsg-2_amd64.deb ... Unpacking spades (3.15.5+dfsg-2) ... Setting up cd-hit (4.8.1-4) ... Setting up libhtscodecs2:amd64 (1.3.0-4) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up liblcms2-2:amd64 (2.14-2) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libboost1.74-dev:amd64 (1.74.0+ds1-20) ... Setting up libicu72:amd64 (72.1-3) ... Setting up liblerc4:amd64 (4.0.0+ds-2) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libgslcblas0:amd64 (2.7.1+dfsg-3+b1) ... Setting up libmurmurhash2:amd64 (1.5-3) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up gawk (1:5.2.1-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up libglib2.0-0:amd64 (2.74.6-2) ... No schema files found: doing nothing. Setting up bwa (0.7.17-7+b2) ... Setting up fonts-lyx (2.3.7-1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:amd64 (1.52.0-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up libgsl27:amd64 (2.7.1+dfsg-3+b1) ... Setting up m4 (1.4.19-3) ... Setting up libqhull-r8.0:amd64 (2020.2-5) ... Setting up libnlopt0:amd64 (2.7.1-4+b4) ... Setting up file (1:5.44-3) ... Setting up libfml0:amd64 (0.1+git20190320.b499514-1+b1) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up unicode-data (15.0.0-1) ... Setting up libxsimd-dev:amd64 (8.1.0-7) ... Setting up libminimap0:amd64 (0.2-7) ... Setting up libfontenc1:amd64 (1:1.1.4-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libexpat1-dev:amd64 (2.5.0-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.4-2) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up libimagequant0:amd64 (2.17.0-1) ... Setting up libproc2-0:amd64 (2:4.0.2-3) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ... Setting up autopoint (0.21-12) ... Setting up libjsoncpp25:amd64 (1.9.5-4) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libbamtools2.5.2:amd64 (2.5.2+dfsg-4) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libcapnp-0.9.2:amd64 (0.9.2-2) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.2.4-0.1) ... Setting up ruby-webrick (1.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libtiff6:amd64 (4.5.0-5) ... Setting up bamtools (2.5.2+dfsg-4) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up mummer (3.23+dfsg-8) ... Setting up libopenjp2-7:amd64 (2.5.0-1+b1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up sgml-base (1.31) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.6.3-1) ... Setting up openssl (3.0.8-1) ... Setting up libwebpmux3:amd64 (1.2.4-0.1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up mailcap (3.70+nmu1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libssw0:amd64 (1.1-13) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up liblocale-gettext-perl (1.07-5) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.11 (3.11.2-6) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libopenblas0-pthread:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libfml-dev:amd64 (0.1+git20190320.b499514-1+b1) ... Setting up mime-support (3.66) ... Setting up libpython3.11:amd64 (3.11.2-6) ... Setting up libtool (2.4.7-5) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libwebpdemux2:amd64 (1.2.4-0.1) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up python3 (3.11.2-1+b1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up python3-tz (2022.7.1-3) ... Setting up bowtie2 (2.5.0-3+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up python3-six (1.16.0-4) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up python3-decorator (5.1.1-3) ... Setting up python3-packaging (23.0-1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libpython3.11-dev:amd64 (3.11.2-6) ... Setting up python3-brotli (1.0.9-2+b6) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-reportlab-accel:amd64 (3.6.12-1+b1) ... Setting up python3-kiwisolver (1.4.4-1+b1) ... Setting up mash (2.3+dfsg-3+b1) ... Setting up libminimap-dev:amd64 (0.2-7) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up python3-pluggy (1.0.0+repack-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libopenblas0:amd64 (0.3.21+ds-4) ... Setting up groff-base (1.22.4-10) ... Setting up xml-core (0.18+nmu1) ... Setting up libxslt1.1:amd64 (1.1.35-1) ... Setting up libx11-6:amd64 (2:1.8.4-2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up python3-dateutil (2.8.2-2) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up python3-appdirs (1.4.4-3) ... Setting up python3-soupsieve (2.3.2-1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-2) ... Setting up libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up dh-python (5.20230130) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.11.1-1) ... Setting up python3-attr (22.2.0-1) ... Setting up libpython3-dev:amd64 (3.11.2-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up python3-py (1.11.0-1) ... Setting up python3-joblib (1.2.0-4) ... Setting up python3-lz4 (4.0.2+dfsg-1+b2) ... Setting up python3.11-dev (3.11.2-6) ... Setting up python3-pytest (7.2.1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3-ply (3.11-5) ... Setting up python3-gast (0.5.2-2) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-yaml (6.0-3+b2) ... Setting up libcurl3-gnutls:amd64 (7.88.1-9) ... Setting up rubygems-integration (1.18) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-bs4 (4.11.2-2) ... Setting up python3-fs (2.4.16-2) ... Setting up python3-beniget (0.4.1-3) ... Setting up libopenblas-dev:amd64 (0.3.21+ds-4) ... Setting up libpython3-all-dev:amd64 (3.11.2-1+b1) ... Setting up libraqm0:amd64 (0.7.0-4.1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-lxml:amd64 (4.9.2-1+b1) ... Setting up python3-contourpy (1.0.7-1+b1) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up python3-dendropy (4.5.2-1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up python3-pysam (0.20.0+ds-3+b1) ... Setting up libtk8.6:amd64 (8.6.13-2) ... Setting up debhelper (13.11.4) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up samtools (1.16.1-1) ... Setting up python3-pil:amd64 (9.4.0-1.1+b1) ... Setting up python3-reportlab (3.6.12-1) ... Setting up python3-pythran (0.11.0+ds-7) ... Setting up spades (3.15.5+dfsg-2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Setting up python3-scipy (1.10.1-2) ... Setting up python3-renderpm:amd64 (3.6.12-1+b1) ... Setting up blt (2.5.3+dfsg-4.1) ... Setting up fastaq (3.17.0-5) ... Setting up python3-tk:amd64 (3.11.2-2) ... Setting up python3-pymummer (0.11.0-3) ... Setting up python3-pil.imagetk:amd64 (9.4.0-1.1+b1) ... Setting up python3-ufolib2 (0.14.0+dfsg1-1) ... Setting up libruby:amd64 (1:3.1) ... Setting up python3-fonttools (4.38.0-1+b1) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b1) ... Setting up libruby3.1:amd64 (3.1.2-7) ... Setting up python3-matplotlib (3.6.3-1+b1) ... Setting up ruby3.1 (3.1.2-7) ... Setting up ruby (1:3.1) ... Setting up ruby-asciidoctor (2.0.18-2) ... Setting up rake (13.0.6-3) ... Setting up asciidoctor (2.0.18-2) ... Setting up ruby-rubygems (3.3.15-2) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.80+dfsg-4+b1) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/ariba-2.14.6+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_2.14.6+ds-5_source.changes dpkg-buildpackage: info: source package ariba dpkg-buildpackage: info: source version 2.14.6+ds-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/ariba-2.14.6+ds' rm -rf /build/ariba-2.14.6+ds/debian/man dh_auto_clean -- I: pybuild base:240: python3.11 setup.py clean running clean removing '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it make[1]: Leaving directory '/build/ariba-2.14.6+ds' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py build running build running build_py creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/samtools_variants.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/assembly.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/assembly_variants.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/reference_data.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/__init__.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/sequence_metadata.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/versions.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/clusters.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/ref_preparer.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/cluster.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/aln_to_metadata.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/mapping.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/ref_genes_getter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/cdhit.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/common.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/faidx.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/mic_plotter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/summary_sample.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/histogram.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/report.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/sequence_variant.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/pubmlst_getter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/read_store.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/tb.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/report_filter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/flag.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/external_progs.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/link.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/summary_cluster_variant.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/mlst_reporter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/megares_zip_parser.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/summary.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/megares_data_finder.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/bam_parse.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/read_filter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/pubmlst_ref_preparer.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/mlst_profile.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/assembly_compare.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/scaffold_graph.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/report_flag_expander.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/vfdb_parser.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/summary_cluster.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/card_record.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/refdata_query.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba copying ariba/ref_seq_chooser.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks copying ariba/tasks/aln2meta.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks copying ariba/tasks/getref.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks copying ariba/tasks/__init__.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks copying ariba/tasks/pubmlstspecies.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks copying ariba/tasks/pubmlstget.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks copying ariba/tasks/test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks copying ariba/tasks/refquery.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks copying ariba/tasks/reportfilter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks copying ariba/tasks/prepareref_tb.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks copying ariba/tasks/micplot.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks copying ariba/tasks/flag.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks copying ariba/tasks/summary.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks copying ariba/tasks/run.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks copying ariba/tasks/prepareref.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks copying ariba/tasks/version.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks copying ariba/tasks/expandflag.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/mapping_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/samtools_variants_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/cluster_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/assembly_variants_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/ncbi_getter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/common_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/__init__.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/scaffold_graph_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/megares_data_finder_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/cdhit_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/ref_seq_chooser_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/megares_zip_parser_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/versions_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/card_record_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/assembly_compare_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/test_refdata_query.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/summary_cluster_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/mlst_profile_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/summary_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/clusters_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/ref_preparer_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/bam_parse_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/external_progs_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/ref_genes_getter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/histogram_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/faidx_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/link_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/flag_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/tb_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/summary_cluster_variant_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/pubmlst_getter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/sequence_metadata_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/sequence_variant_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/assembly_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/aln_to_metadata_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/read_filter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/mlst_reporter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/report_filter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/summary_sample_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/mic_plotter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/report_flag_expander_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/read_store_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/reference_data_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/vfdb_parser_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests copying ariba/tests/pubmlst_ref_preparer_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/test_run_data copying ariba/test_run_data/ref_seqs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/test_run_data copying ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/test_run_data copying ariba/test_run_data/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/test_run_data copying ariba/test_run_data/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/test_run_data copying ariba/test_run_data/metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/test_run_data creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tb_data copying ariba/tb_data/NC_000962.3.fa.gz -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181115.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181221.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20190102.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tb_data copying ariba/tb_data/NC_000962.3.gb -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181115.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181221.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20190102.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tb_data creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_count_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_ok.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_whole_run.in.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.rename.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.smi -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_write_report.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_init.fofn -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_run.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_fasta_file.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_write_all_links_to_file.out -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_load_report_bad.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/vfdb_parser_test_run.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/report_flag_expander.run.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/vfdb_parser_test_run.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.profile.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_init_good.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_rename_seqs.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.read_store -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.in.1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.in.2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence_type.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.in.3 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_fails.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_cat_genes_match_ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_rename_sequences.out -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.4.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/refdata_query_prepareref.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_load_report_good.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_init_refdata.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.out.cluster -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_load_mic_file.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_sort_file.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.ariba.report.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.params.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_db.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_load_annotations.csv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_fails.empty.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.3.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_report.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_load_summary_file.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.removed.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_load_file.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_sort_file.out -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_insert_codon.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_load_input_files.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.2.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_whole_run.in.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_fasta_files.in.1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_write_distance_matrix.distances -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.1.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence_type.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_count_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.out -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parse_extract_files_ok.zip -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_rename_sequences.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.ref.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite.expected.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite.expected.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_compress_and_index_file.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_getter.dbases.xml -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_data_info_file -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/summary_to_matrix.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_fails.empty.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_whole_run.out.csv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_fake_run.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_check_spades_log_file.log.bad -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/refdata_query_prepareref.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_load_fofn -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_init_refdata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/tb_genbank_to_gene_coords.gb -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_metadata_tsvs.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_db.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/report_flag_expander.run.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_profile_test.init.profile.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.rename -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_remove_bad_genes.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_rename_file.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_sam_to_fastq.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_too_short.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite.reads.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_run.expected.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_too_long.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_var_groups.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_load_input_files.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_clean.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/dummy.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/tb_report_to_resistance_dict.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/summary_to_matrix.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_profile_test.profile.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/vfdb_parser_test_run.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_not_gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_init_bad.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variants.vcf -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_unsorted.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/00.info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/00.rename_info -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/00.info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/00.info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/00.params.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail copying ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly copying ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/megares_zip_parser_write_files creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2 copying ariba/tests/data/cluster_test_init_no_reads_2/genes.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2 creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1 copying ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1 creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_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/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene running build_ext building 'minimap_ariba' extension creating build creating build/temp.linux-x86_64-cpython-311 creating build/temp.linux-x86_64-cpython-311/ariba creating build/temp.linux-x86_64-cpython-311/ariba/ext x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/ariba-2.14.6+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/minimap -I/usr/include/python3.11 -c ariba/ext/minimap_ariba.cpp -o build/temp.linux-x86_64-cpython-311/ariba/ext/minimap_ariba.o ariba/ext/minimap_ariba.cpp: In function 'bool readMappingOk(const mm_reg1_t*, const mm_idx_t*, const kseq_t*, uint32_t)': ariba/ext/minimap_ariba.cpp:371:23: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 371 | if (r->qe - r->qs < std::min((unsigned) 50, (int) 0.5 * ks->seq.l)) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:381:26: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 381 | startOk = (r->qs < endTolerance || refLength - r->re < endTolerance); | ~~~~~~^~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:382:60: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 382 | endOk = (ks->seq.l - r->qe < endTolerance || r->rs < endTolerance); | ~~~~~~^~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:386:26: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 386 | startOk = (r->qs < endTolerance || r->rs < endTolerance); | ~~~~~~^~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:386:50: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 386 | startOk = (r->qs < endTolerance || r->rs < endTolerance); | ~~~~~~^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/ariba-2.14.6+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/ariba/ext/minimap_ariba.o -L/usr/lib/x86_64-linux-gnu -o /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/minimap_ariba.cpython-311-x86_64-linux-gnu.so -lz -lminimap building 'fermilite_ariba' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/ariba-2.14.6+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c ariba/ext/fml-asm_ariba.cpp -o build/temp.linux-x86_64-cpython-311/ariba/ext/fml-asm_ariba.o x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/ariba-2.14.6+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/ariba/ext/fml-asm_ariba.o -L/usr/lib/x86_64-linux-gnu -o /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/fermilite_ariba.cpython-311-x86_64-linux-gnu.so -lz -lfml building 'vcfcall_ariba' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/ariba-2.14.6+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c ariba/ext/vcfcall_ariba.cpp -o build/temp.linux-x86_64-cpython-311/ariba/ext/vcfcall_ariba.o x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/ariba-2.14.6+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/ariba/ext/vcfcall_ariba.o -L/usr/lib/x86_64-linux-gnu -o /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/vcfcall_ariba.cpython-311-x86_64-linux-gnu.so running build_scripts creating build/scripts-3.11 copying and adjusting scripts/ariba -> build/scripts-3.11 changing mode of build/scripts-3.11/ariba from 644 to 755 dh_auto_test -O--buildsystem=pybuild I: pybuild base:240: cd /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build; python3.11 -m pytest ============================= test session starts ============================== platform linux -- Python 3.11.2, pytest-7.2.1, pluggy-1.0.0+repack rootdir: /build/ariba-2.14.6+ds, configfile: pytest.ini collected 356 items ariba/tests/aln_to_metadata_test.py .................... [ 5%] ariba/tests/assembly_compare_test.py ................ [ 10%] ariba/tests/assembly_test.py ......... [ 12%] ariba/tests/assembly_variants_test.py ........... [ 15%] ariba/tests/bam_parse_test.py ...... [ 17%] ariba/tests/card_record_test.py ........ [ 19%] ariba/tests/cdhit_test.py ................ [ 24%] ariba/tests/cluster_test.py sssssssssssssssssssssssssssss [ 32%] ariba/tests/clusters_test.py ................ [ 36%] ariba/tests/common_test.py .. [ 37%] ariba/tests/external_progs_test.py . [ 37%] ariba/tests/faidx_test.py . [ 37%] ariba/tests/flag_test.py ....... [ 39%] ariba/tests/histogram_test.py .... [ 41%] ariba/tests/link_test.py ......... [ 43%] ariba/tests/mapping_test.py ..ss... [ 45%] ariba/tests/megares_data_finder_test.py .. [ 46%] ariba/tests/megares_zip_parser_test.py ..... [ 47%] ariba/tests/mic_plotter_test.py ............. [ 51%] ariba/tests/mlst_profile_test.py .... [ 52%] ariba/tests/mlst_reporter_test.py ..... [ 53%] ariba/tests/pubmlst_getter_test.py ... [ 54%] ariba/tests/pubmlst_ref_preparer_test.py .. [ 55%] ariba/tests/read_filter_test.py . [ 55%] ariba/tests/read_store_test.py ....... [ 57%] ariba/tests/ref_genes_getter_test.py . [ 57%] ariba/tests/ref_preparer_test.py ..... [ 58%] ariba/tests/ref_seq_chooser_test.py ....... [ 60%] ariba/tests/reference_data_test.py .............................. [ 69%] ariba/tests/report_filter_test.py ................. [ 74%] ariba/tests/report_flag_expander_test.py . [ 74%] ariba/tests/samtools_variants_test.py s...s.. [ 76%] ariba/tests/scaffold_graph_test.py ..... [ 77%] ariba/tests/sequence_metadata_test.py ..... [ 79%] ariba/tests/sequence_variant_test.py ....... [ 81%] ariba/tests/summary_cluster_test.py ....................... [ 87%] ariba/tests/summary_cluster_variant_test.py .... [ 88%] ariba/tests/summary_sample_test.py .... [ 89%] ariba/tests/summary_test.py .................... [ 95%] ariba/tests/tb_test.py ....... [ 97%] ariba/tests/test_refdata_query.py ..... [ 98%] ariba/tests/versions_test.py . [ 99%] ariba/tests/vfdb_parser_test.py ... [100%] =============================== warnings summary =============================== ariba/external_progs.py:34 /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/external_progs.py:34: DeprecationWarning: invalid escape sequence '\.' 'cdhit': ('', re.compile('CD-HIT version ([0-9\.]+) \(')), ariba/external_progs.py:35 /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/external_progs.py:35: DeprecationWarning: invalid escape sequence '\.' 'nucmer': ('--version', re.compile('([0-9]+\.[0-9\.]+.*$)')), ariba/external_progs.py:36 /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/external_progs.py:36: DeprecationWarning: invalid escape sequence '\s' 'spades': ('--version', re.compile('SPAdes\s+v([0-9\.]+)')) ../../../../../usr/lib/python3/dist-packages/dendropy/utility/textprocessing.py:42 /usr/lib/python3/dist-packages/dendropy/utility/textprocessing.py:42: DeprecationWarning: Use setlocale(), getencoding() and getlocale() instead ENCODING = locale.getdefaultlocale()[1] ariba/external_progs.py:88: 30 warnings .pybuild/cpython3_3.11_ariba/build/ariba/tests/assembly_test.py: 24 warnings .pybuild/cpython3_3.11_ariba/build/ariba/tests/cdhit_test.py: 60 warnings .pybuild/cpython3_3.11_ariba/build/ariba/tests/external_progs_test.py: 6 warnings .pybuild/cpython3_3.11_ariba/build/ariba/tests/pubmlst_ref_preparer_test.py: 6 warnings .pybuild/cpython3_3.11_ariba/build/ariba/tests/read_filter_test.py: 6 warnings .pybuild/cpython3_3.11_ariba/build/ariba/tests/ref_preparer_test.py: 54 warnings .pybuild/cpython3_3.11_ariba/build/ariba/tests/reference_data_test.py: 36 warnings .pybuild/cpython3_3.11_ariba/build/ariba/tests/tb_test.py: 12 warnings .pybuild/cpython3_3.11_ariba/build/ariba/tests/versions_test.py: 6 warnings /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/external_progs.py:88: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. if prog in min_versions and LooseVersion(version) < LooseVersion(min_versions[prog]): .pybuild/cpython3_3.11_ariba/build/ariba/tests/clusters_test.py: 8 warnings .pybuild/cpython3_3.11_ariba/build/ariba/tests/mapping_test.py: 2 warnings /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/mapping.py:86: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. if LooseVersion(bowtie2_version) >= LooseVersion('2.3.1'): .pybuild/cpython3_3.11_ariba/build/ariba/tests/megares_data_finder_test.py::TestMegaresDataFinder::test_get_url_for_version .pybuild/cpython3_3.11_ariba/build/ariba/tests/megares_data_finder_test.py::TestMegaresDataFinder::test_get_url_for_version /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/megares_data_finder.py:50: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. versions.sort(key=LooseVersion) .pybuild/cpython3_3.11_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours .pybuild/cpython3_3.11_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours .pybuild/cpython3_3.11_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/mic_plotter.py:222: PendingDeprecationWarning: The get_cmap function will be deprecated in a future version. Use ``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap(obj)`` instead. cmap = cmx.get_cmap(colormap) .pybuild/cpython3_3.11_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/mic_plotter.py:206: PendingDeprecationWarning: The get_cmap function will be deprecated in a future version. Use ``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap(obj)`` instead. cmap = cmx.get_cmap(colormap) .pybuild/cpython3_3.11_ariba/build/ariba/tests/pubmlst_ref_preparer_test.py: 5 warnings .pybuild/cpython3_3.11_ariba/build/ariba/tests/versions_test.py: 5 warnings /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/versions.py:46: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. if package in package_min_versions and LooseVersion(version) < package_min_versions[package]: .pybuild/cpython3_3.11_ariba/build/ariba/tests/pubmlst_ref_preparer_test.py: 5 warnings .pybuild/cpython3_3.11_ariba/build/ariba/tests/versions_test.py: 5 warnings /usr/lib/python3/dist-packages/setuptools/_distutils/version.py:346: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. other = LooseVersion(other) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========== 323 passed, 33 skipped, 280 warnings in 85.30s (0:01:25) =========== create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/ariba/ -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/ariba-2.14.6+ds/debian/ariba running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running build_ext running build_scripts running install_lib creating /build/ariba-2.14.6+ds/debian/ariba/usr creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11 creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/vcfcall_ariba.cpython-311-x86_64-linux-gnu.so -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/fermilite_ariba.cpython-311-x86_64-linux-gnu.so -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/minimap_ariba.cpython-311-x86_64-linux-gnu.so -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/summary.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/report_flag_expander.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/vfdb_parser.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/ref_genes_getter.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/refdata_query.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/read_filter.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/versions.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/pubmlst_ref_preparer.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/pubmlst_getter.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/mic_plotter.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/megares_zip_parser.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/megares_data_finder.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/faidx.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/ref_preparer.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/tb.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/sequence_metadata.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/reference_data.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/report_filter.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/read_store.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/summary_cluster_variant.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/summary_cluster.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/summary_sample.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/mlst_profile.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/mlst_reporter.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/histogram.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/clusters.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/samtools_variants.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/report.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/flag.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/cluster.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/cdhit.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/card_record.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/assembly_variants.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/assembly_compare.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/ref_seq_chooser.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/external_progs.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/link.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/scaffold_graph.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/bam_parse.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/mapping.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/common.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/assembly.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/sequence_variant.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/aln_to_metadata.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__pycache__/__init__.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__pycache__ creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tb_data/panel.20190102.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tb_data/panel.20181221.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tb_data/panel.20181115.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tb_data/NC_000962.3.gb -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tb_data/panel.20190102.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tb_data/panel.20181221.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tb_data/panel.20181115.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tb_data/NC_000962.3.fa.gz -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tb_data creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/test_run_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/test_run_data/metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/test_run_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/test_run_data/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/test_run_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/test_run_data/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/test_run_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/test_run_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/test_run_data/ref_seqs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/test_run_data creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/vfdb_parser_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/versions_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/test_refdata_query.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/tb_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/summary_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/summary_sample_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/summary_cluster_variant_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/summary_cluster_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/sequence_variant_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/sequence_metadata_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/scaffold_graph_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/samtools_variants_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/report_flag_expander_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/report_filter_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/reference_data_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/ref_seq_chooser_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/ref_preparer_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/ref_genes_getter_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/read_store_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/read_filter_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/pubmlst_ref_preparer_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/pubmlst_getter_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/ncbi_getter_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/mlst_reporter_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/mlst_profile_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/mic_plotter_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/megares_zip_parser_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/megares_data_finder_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/mapping_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/link_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/histogram_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/flag_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/faidx_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/external_progs_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/common_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/clusters_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/cluster_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/cdhit_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/card_record_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/bam_parse_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/assembly_variants_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/assembly_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/assembly_compare_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/aln_to_metadata_test.cpython-311-pytest-7.2.1.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__pycache__/__init__.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__pycache__ creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1 creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2/genes.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2 creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/megares_zip_parser_write_files copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/megares_zip_parser_write_files copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/megares_zip_parser_write_files copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/megares_zip_parser_write_files creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/profile.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene2.tfa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.params.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/clusters_run_with_tb.ref creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.version_info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.rename_info -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out/00.info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/ref_preparer_test_run.out creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref/00.rename_info -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref/00.info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mapping_test_bowtie2_unsorted.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.vcf -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/report_filter_test_init_bad.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refcheck_test_check_not_gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/vfdb_parser_test_run.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_profile_test.profile.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/summary_to_matrix.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/tb_report_to_resistance_dict.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/dummy.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/link_test_init.reads.no_link.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_store_test_clean.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/link_test_init.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/summary_test_load_input_files.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/summary_sample_test_var_groups.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refcheck_test_check_too_long.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/report_filter_test_run.expected.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_run_fermilite.reads.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refcheck_test_check_too_short.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mapping_test_sam_to_fastq.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cdhit_test_run.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_dummy_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_load_rename_file.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_test_remove_bad_genes.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refcheck_test_fix_out.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refcheck_test_fix_out.rename -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_profile_test.init.profile.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/report_flag_expander.run.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_init_ok.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_dummy_db.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_load_all_metadata_tsvs.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/tb_genbank_to_gene_coords.gb -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_init_refdata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/link_test_init.reads.make_link_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/summary_test_load_fofn -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_test_check_spades_log_file.log.bad -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cdhit_test_fake_run.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/summary_test_whole_run.out.csv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_init_fails.empty.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/summary_to_matrix.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_load_data_info_file -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mapping_test_bowtie2_ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/pubmlst_getter.dbases.xml -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_store_test_compress_and_index_file.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_sequence.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_run_fermilite.expected.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_run_fermilite.expected.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/link_test_init.ref.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_rename_sequences.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/megares_zip_parse_extract_files_ok.zip -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/graph_test_update_from_sam.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/test_common_cat_files.out -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/link_test_init.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_count_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_sequence_type.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.in.1.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/summary_test_write_distance_matrix.distances -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refcheck_test_fix_out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/link_test_init.reads.no_link_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_sequence.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_load_all_fasta_files.in.1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/summary_test_whole_run.in.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.in.2.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/summary_test_load_input_files.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_store_test_sort_file.out -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/summary_sample_test_load_file.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/link_test_init.reads.no_link_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/link_test_init.reads.make_link_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refcheck_test_fix_out.removed.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mic_plotter_load_summary_file.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_init_ok.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_write_report.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.in.3.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_init_fails.empty.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/megares_zip_parser_load_annotations.csv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_dummy_db.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_init_ok.params.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.ariba.report.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_dummy_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mapping_test_bowtie2_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_store_test_sort_file.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mic_plotter_load_mic_file.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_store_test_get_reads.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.cluster -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refcheck_test_fix_in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_init_refdata.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/report_filter_test_load_report_good.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/bam_parse_test_parse.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refdata_query_prepareref.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.in.4.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_test_rename_sequences.out -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/link_test_init.reads.make_link.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_cat_genes_match_ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_init_fails.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/test_common_cat_files.in.3 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_sequence_type.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/test_common_cat_files.in.2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/link_test_init.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/test_common_cat_files.in.1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_filter_test_run.in.read_store -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/pubmlst_rename_seqs.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/report_filter_test_init_good.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_reporter.profile.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_preparer_test_run.in.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/vfdb_parser_test_run.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/report_flag_expander.run.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/vfdb_parser_test_run.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/report_filter_test_load_report_bad.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/graph_test_write_all_links_to_file.out -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_load_fasta_file.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/report_filter_test_run.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/summary_test_init.fofn -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/report_filter_test_write_report.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.smi -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_init_ok.rename.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/read_filter_test_run.in.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/summary_test_whole_run.in.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/bam_parse_test_parse.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/bam_parse_test_parse.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_filter_bad_data.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/refcheck_test_check_ok.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/graph_test_update_from_sam.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cluster_test_count_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/pubmlst_ref_preparer_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/vfdb_parser_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/reference_data_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/read_store_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/report_flag_expander_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/mic_plotter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/summary_sample_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/report_filter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/mlst_reporter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/read_filter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/aln_to_metadata_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/assembly_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/sequence_variant_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/sequence_metadata_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/pubmlst_getter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/summary_cluster_variant_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/tb_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/flag_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/link_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/faidx_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/histogram_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/ref_genes_getter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/external_progs_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/bam_parse_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/ref_preparer_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/clusters_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/summary_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/mlst_profile_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/summary_cluster_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/test_refdata_query.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/assembly_compare_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/card_record_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/versions_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/megares_zip_parser_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/ref_seq_chooser_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/cdhit_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/megares_data_finder_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/scaffold_graph_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/__init__.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/common_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/ncbi_getter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/assembly_variants_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/cluster_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/samtools_variants_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tests/mapping_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/__pycache__/version.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/__pycache__/test.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/__pycache__/summary.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/__pycache__/run.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/__pycache__/reportfilter.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/__pycache__/refquery.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/__pycache__/pubmlstspecies.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/__pycache__/pubmlstget.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/__pycache__/prepareref_tb.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/__pycache__/prepareref.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/__pycache__/micplot.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/__pycache__/getref.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/__pycache__/flag.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/__pycache__/expandflag.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/__pycache__/aln2meta.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/__pycache__/__init__.cpython-311.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/expandflag.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/version.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/prepareref.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/run.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/summary.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/flag.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/micplot.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/prepareref_tb.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/reportfilter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/refquery.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/pubmlstget.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/pubmlstspecies.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/__init__.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/getref.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tasks/aln2meta.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/ref_seq_chooser.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/refdata_query.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/card_record.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/summary_cluster.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/vfdb_parser.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/report_flag_expander.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/scaffold_graph.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/assembly_compare.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/mlst_profile.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/pubmlst_ref_preparer.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/read_filter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/bam_parse.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/megares_data_finder.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/summary.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/megares_zip_parser.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/mlst_reporter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/summary_cluster_variant.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/link.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/external_progs.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/flag.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/report_filter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/tb.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/read_store.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/pubmlst_getter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/sequence_variant.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/report.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/histogram.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/summary_sample.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/mic_plotter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/faidx.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/common.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/cdhit.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/ref_genes_getter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/mapping.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/aln_to_metadata.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/cluster.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/ref_preparer.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/clusters.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/versions.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/sequence_metadata.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/__init__.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/reference_data.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/assembly_variants.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/assembly.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.11_ariba/build/ariba/samtools_variants.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/pubmlst_ref_preparer_test.py to pubmlst_ref_preparer_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/vfdb_parser_test.py to vfdb_parser_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/reference_data_test.py to reference_data_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/read_store_test.py to read_store_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/report_flag_expander_test.py to report_flag_expander_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/mic_plotter_test.py to mic_plotter_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/summary_sample_test.py to summary_sample_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/report_filter_test.py to report_filter_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/mlst_reporter_test.py to mlst_reporter_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/read_filter_test.py to read_filter_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/aln_to_metadata_test.py to aln_to_metadata_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/assembly_test.py to assembly_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/sequence_variant_test.py to sequence_variant_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/sequence_metadata_test.py to sequence_metadata_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/pubmlst_getter_test.py to pubmlst_getter_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/summary_cluster_variant_test.py to summary_cluster_variant_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/tb_test.py to tb_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/flag_test.py to flag_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/link_test.py to link_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/faidx_test.py to faidx_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/histogram_test.py to histogram_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/ref_genes_getter_test.py to ref_genes_getter_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/external_progs_test.py to external_progs_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/bam_parse_test.py to bam_parse_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/ref_preparer_test.py to ref_preparer_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/clusters_test.py to clusters_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/summary_test.py to summary_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/mlst_profile_test.py to mlst_profile_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/summary_cluster_test.py to summary_cluster_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/test_refdata_query.py to test_refdata_query.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/assembly_compare_test.py to assembly_compare_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/card_record_test.py to card_record_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/versions_test.py to versions_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/megares_zip_parser_test.py to megares_zip_parser_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/ref_seq_chooser_test.py to ref_seq_chooser_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/cdhit_test.py to cdhit_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/megares_data_finder_test.py to megares_data_finder_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/scaffold_graph_test.py to scaffold_graph_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/__init__.py to __init__.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/common_test.py to common_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/ncbi_getter_test.py to ncbi_getter_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/assembly_variants_test.py to assembly_variants_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/cluster_test.py to cluster_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/samtools_variants_test.py to samtools_variants_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tests/mapping_test.py to mapping_test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/expandflag.py to expandflag.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/version.py to version.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/prepareref.py to prepareref.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/run.py to run.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/summary.py to summary.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/flag.py to flag.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/micplot.py to micplot.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/prepareref_tb.py to prepareref_tb.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/reportfilter.py to reportfilter.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/refquery.py to refquery.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/test.py to test.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/pubmlstget.py to pubmlstget.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/pubmlstspecies.py to pubmlstspecies.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/__init__.py to __init__.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/getref.py to getref.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tasks/aln2meta.py to aln2meta.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/ref_seq_chooser.py to ref_seq_chooser.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/refdata_query.py to refdata_query.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/card_record.py to card_record.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/summary_cluster.py to summary_cluster.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/vfdb_parser.py to vfdb_parser.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/report_flag_expander.py to report_flag_expander.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/scaffold_graph.py to scaffold_graph.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/assembly_compare.py to assembly_compare.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/mlst_profile.py to mlst_profile.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/pubmlst_ref_preparer.py to pubmlst_ref_preparer.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/read_filter.py to read_filter.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/bam_parse.py to bam_parse.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/megares_data_finder.py to megares_data_finder.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/summary.py to summary.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/megares_zip_parser.py to megares_zip_parser.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/mlst_reporter.py to mlst_reporter.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/summary_cluster_variant.py to summary_cluster_variant.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/link.py to link.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/external_progs.py to external_progs.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/flag.py to flag.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/report_filter.py to report_filter.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/tb.py to tb.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/read_store.py to read_store.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/pubmlst_getter.py to pubmlst_getter.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/sequence_variant.py to sequence_variant.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/report.py to report.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/histogram.py to histogram.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/summary_sample.py to summary_sample.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/mic_plotter.py to mic_plotter.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/faidx.py to faidx.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/common.py to common.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/cdhit.py to cdhit.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/ref_genes_getter.py to ref_genes_getter.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/mapping.py to mapping.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/aln_to_metadata.py to aln_to_metadata.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/cluster.py to cluster.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/ref_preparer.py to ref_preparer.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/clusters.py to clusters.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/versions.py to versions.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/sequence_metadata.py to sequence_metadata.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/__init__.py to __init__.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/reference_data.py to reference_data.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/assembly_variants.py to assembly_variants.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/assembly.py to assembly.cpython-311.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba/samtools_variants.py to samtools_variants.cpython-311.pyc running install_egg_info running egg_info creating ariba.egg-info writing ariba.egg-info/PKG-INFO writing dependency_links to ariba.egg-info/dependency_links.txt writing requirements to ariba.egg-info/requires.txt writing top-level names to ariba.egg-info/top_level.txt writing manifest file 'ariba.egg-info/SOURCES.txt' reading manifest file 'ariba.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.h' under directory 'third_party' adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'ariba.egg-info/SOURCES.txt' Copying ariba.egg-info to /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.11/dist-packages/ariba-2.14.6.egg-info Skipping SOURCES.txt running install_scripts creating /build/ariba-2.14.6+ds/debian/ariba/usr/bin copying build/scripts-3.11/ariba -> /build/ariba-2.14.6+ds/debian/ariba/usr/bin changing mode of /build/ariba-2.14.6+ds/debian/ariba/usr/bin/ariba to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/ariba-2.14.6+ds' mkdir -p /build/ariba-2.14.6+ds/debian/man asciidoctor -a docdate='' -b manpage -o /build/ariba-2.14.6+ds/debian/man/ariba.1 /build/ariba-2.14.6+ds/debian/ariba.1.adoc dh_installman -- make[1]: Leaving directory '/build/ariba-2.14.6+ds' dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'ariba' in '../ariba_2.14.6+ds-5_amd64.deb'. dpkg-deb: building package 'ariba-dbgsym' in '../ariba-dbgsym_2.14.6+ds-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../ariba_2.14.6+ds-5_amd64.buildinfo dpkg-genchanges --build=binary -O../ariba_2.14.6+ds-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration 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/2494563 and its subdirectories I: Current time: Wed May 3 10:50:31 -12 2023 I: pbuilder-time-stamp: 1683154231