Sun May 26 18:25:00 UTC 2024 I: starting to build circlator/unstable/amd64 on jenkins on '2024-05-26 18:24' Sun May 26 18:25:00 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_4/21452/console.log Sun May 26 18:25:00 UTC 2024 I: Downloading source for unstable/circlator=1.5.6-11 --2024-05-26 18:25:00-- http://deb.debian.org/debian/pool/main/c/circlator/circlator_1.5.6-11.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1672 (1.6K) [text/prs.lines.tag] Saving to: ‘circlator_1.5.6-11.dsc’ 0K . 100% 268M=0s 2024-05-26 18:25:00 (268 MB/s) - ‘circlator_1.5.6-11.dsc’ saved [1672/1672] Sun May 26 18:25:00 UTC 2024 I: circlator_1.5.6-11.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: circlator Binary: circlator Architecture: all Version: 1.5.6-11 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://sanger-pathogens.github.io/circlator/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/circlator Vcs-Git: https://salsa.debian.org/med-team/circlator.git Testsuite: autopkgtest Testsuite-Triggers: python3-all, python3-pytest, spades Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all, python3-setuptools, python3-packaging, python3-openpyxl, python3-jdcal, python3-pysam, python3-pymummer, python3-pytest , fastaq , spades , bwa , prodigal , canu Package-List: circlator deb science optional arch=all Checksums-Sha1: 4b152777c1f475f34867b6014f04efc69d467eb2 5724413 circlator_1.5.6.orig.tar.gz da5bc44f47a7f27a460a0528cb20e80629ae6f96 6152 circlator_1.5.6-11.debian.tar.xz Checksums-Sha256: 1c6ea4f3dfd726cf798b7b3a23e1cb02ade0471597c412b119de8be73db804b6 5724413 circlator_1.5.6.orig.tar.gz 78767aac30c7ed43a3090385949af89050a1fb31e98b8d2c53a32cbe776b7566 6152 circlator_1.5.6-11.debian.tar.xz Files: dbb1ab9bf8d9834fa9106dc99e85d76e 5724413 circlator_1.5.6.orig.tar.gz ee96aaac90403128dd77022a4da2e9fb 6152 circlator_1.5.6-11.debian.tar.xz -----BEGIN PGP SIGNATURE----- iHUEARYIAB0WIQSglbZu4JAkvuai8HIqJ5BL1yQ+2gUCZWukBQAKCRAqJ5BL1yQ+ 2p+NAQDD6Xbyj2MoCciqWr3uoP3V612X9rL5CoyuIH2wgmW5vwEA1RrkwXeaklFO O6LXJYTBHLN63XyGf7mhxKkdkrLjeQQ= =Y8AE -----END PGP SIGNATURE----- Sun May 26 18:25:00 UTC 2024 I: Checking whether the package is not for us Sun May 26 18:25:00 UTC 2024 I: Starting 1st build on remote node ionos15-amd64.debian.net. Sun May 26 18:25:00 UTC 2024 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Sun May 26 18:26:20 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Jun 28 12:48:02 -12 2025 I: pbuilder-time-stamp: 1751158082 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [circlator_1.5.6-11.dsc] I: copying [./circlator_1.5.6.orig.tar.gz] I: copying [./circlator_1.5.6-11.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Dec 2 21:39:17 2023 gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./circlator_1.5.6-11.dsc: no acceptable signature found dpkg-source: info: extracting circlator in circlator-1.5.6 dpkg-source: info: unpacking circlator_1.5.6.orig.tar.gz dpkg-source: info: unpacking circlator_1.5.6-11.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_canu_detection.patch dpkg-source: info: applying switch-to-pytest.patch dpkg-source: info: applying split_canu_tests dpkg-source: info: applying remove-distutils.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1108397/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='b90e608399fb473ca26886583506936d' 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='1108397' 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.wQQTTAFS/pbuilderrc_Mqne --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wQQTTAFS/b1 --logfile b1/build.log circlator_1.5.6-11.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 28 14:05 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1108397/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-sequence-python3, python3-all, python3-setuptools, python3-packaging, python3-openpyxl, python3-jdcal, python3-pysam, python3-pymummer, python3-pytest, fastaq, spades, bwa, prodigal, canu dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19718 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-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-packaging; however: Package python3-packaging is not installed. pbuilder-satisfydepends-dummy depends on python3-openpyxl; however: Package python3-openpyxl is not installed. pbuilder-satisfydepends-dummy depends on python3-jdcal; however: Package python3-jdcal is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-pymummer; however: Package python3-pymummer is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on fastaq; however: Package fastaq is not installed. pbuilder-satisfydepends-dummy depends on spades; however: Package spades is not installed. pbuilder-satisfydepends-dummy depends on bwa; however: Package bwa is not installed. pbuilder-satisfydepends-dummy depends on prodigal; however: Package prodigal is not installed. pbuilder-satisfydepends-dummy depends on canu; however: Package canu 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: aglfn{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bamtools{a} binfmt-support{a} bsdextrautils{a} bwa{a} ca-certificates{a} ca-certificates-java{a} canu{a} debhelper{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fastaq{a} fastjar{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gawk{a} gettext{a} gettext-base{a} gnuplot-data{a} gnuplot-nox{a} groff-base{a} intltool-debian{a} jaligner{a} jarwrapper{a} java-common{a} libabsl20230802{a} libaom3{a} libapache-pom-java{a} libarchive-zip-perl{a} libatinject-jsr330-api-java{a} libavif16{a} libbamtools2.5.2{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcom-err2{a} libcommons-compress-java{a} libcommons-parent-java{a} libcurl3t64-gnutls{a} libdatrie1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1t64{a} liberror-prone-java{a} libexpat1{a} libfastutil-java{a} libfile-stripnondeterminism-perl{a} libfilesys-df-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libguava-java{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libjsoncpp25{a} libjsr305-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblua5.4-0{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnlopt0{a} libnspr4{a} libnss3{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpcsclite1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} librav1e0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsigsegv2{a} libsnappy1v5{a} libssh2-1t64{a} libssw-java{a} libssw0{a} libsvtav1enc1d1{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxpm4{a} libxrender1{a} libxslt1.1{a} libyaml-0-2{a} libyuv0{a} m4{a} man-db{a} media-types{a} mhap{a} mummer{a} netbase{a} openjdk-17-jre-headless{a} openssl{a} po-debconf{a} procps{a} prodigal{a} python3{a} python3-all{a} python3-distutils{a} python3-et-xmlfile{a} python3-iniconfig{a} python3-jdcal{a} python3-joblib{a} python3-lib2to3{a} python3-lxml{a} python3-minimal{a} python3-openpyxl{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pymummer{a} python3-pysam{a} python3-pytest{a} python3-setuptools{a} python3-yaml{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} samtools{a} sensible-utils{a} spades{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-liberation groff krb5-locales libarchive-cpio-perl libasound2t64 libcups2t64 libglib2.0-data libgpm2 libheif-plugin-aomenc libheif-plugin-x265 libldap-common libltdl-dev libmail-sendmail-perl liboss4-salsa-asound2 libsasl2-modules lynx psmisc publicsuffix python3-bs4 python3-cssselect python3-html5lib python3-numpy python3-pil python3-psutil python3-pygments python3-simplejson shared-mime-info wget xdg-user-dirs 0 packages upgraded, 182 newly installed, 0 to remove and 0 not upgraded. Need to get 147 MB of archives. After unpacking 549 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 binfmt-support amd64 2.2.2-7 [64.3 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libsigsegv2 amd64 2.14-1+b1 [34.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 gawk amd64 1:5.2.1-2+b1 [674 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 17 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.3-1 [809 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.3-1 [2139 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.1-1 [94.1 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 aglfn all 1.7+git20191031.4036a9c-2 [30.5 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-5 [159 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 bamtools amd64 2.5.2+dfsg-5 [206 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 bwa amd64 0.7.17-7+b3 [212 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.2.1-1 [29.1 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libfilesys-df-perl amd64 0.92-7+b3 [11.8 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 java-common all 0.75 [6640 B] Get: 47 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.100-1 [1406 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.2.2-1 [54.9 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jre-headless amd64 17.0.11+9-1 [43.8 MB] Get: 53 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B] Get: 54 http://deb.debian.org/debian unstable/main amd64 fastjar amd64 2:0.98-7 [80.1 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 jarwrapper all 0.79 [10.1 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 57 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libcommons-compress-java all 1.25.0-1 [635 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libfastutil-java all 8.5.12+dfsg-2 [19.6 MB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 61 http://deb.debian.org/debian unstable/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 jaligner all 1.0+dfsg-11 [133 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libssw-java amd64 1.1-14+b1 [18.2 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 mhap all 2.1.3+dfsg-3 [160 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 gnuplot-data all 6.0.0+dfsg1-3 [72.3 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240517-1 [93.3 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.8.2-2 [1869 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.4.1-1 [547 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-2+b1 [351 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 librav1e0 amd64 0.7.1-2 [900 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc1d1 amd64 1.7.0+dfsg-2+b1 [2169 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1888.20240509-4 [170 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.0.4-3 [106 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.17.6-1+b2 [9856 B] Get: 98 http://deb.debian.org/debian unstable/main amd64 libde265-0 amd64 1.0.15-1+b1 [187 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.17.6-1+b2 [13.1 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libheif1 amd64 1.17.6-1+b2 [284 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libgd3 amd64 2.3.3-9+b3 [125 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.80.2-2 [1485 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 liblua5.4-0 amd64 5.4.6-3+b1 [147 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.52.2+ds-1 [218 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.52.2+ds-1 [48.1 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.52.2+ds-1 [35.0 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.4.0-0.1 [123 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 gnuplot-nox amd64 6.0.0+dfsg1-3 [916 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 canu amd64 2.2+dfsg-5 [1413 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 129 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-2 [670 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-3.1 [77.7 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-3.1 [131 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240422 [107 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 146 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-5 [215 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.8.0-1 [434 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.19.2-1+b1 [645 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 fastaq all 3.17.0-6 [47.5 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libnlopt0 amd64 2.7.1-5+b3 [174 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.3-1 [1951 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-14+b1 [21.2 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1+b1 [232 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 mummer amd64 3.23+dfsg-8 [662 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 prodigal amd64 1:2.6.3-6 [508 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.3-1 [659 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.11.8-1 [1056 B] Get: 170 http://deb.debian.org/debian unstable/main amd64 python3-et-xmlfile all 1.0.1-2.1 [9180 B] Get: 171 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 172 http://deb.debian.org/debian unstable/main amd64 python3-jdcal all 1.0-1.3 [7904 B] Get: 173 http://deb.debian.org/debian unstable/main amd64 python3-joblib all 1.3.2-2 [218 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 5.2.1-1 [1995 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 python3-openpyxl all 3.1.2+dfsg-6 [165 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 python3-pymummer all 0.11.0-4 [18.0 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 python3-pysam amd64 0.22.1+ds-1 [4654 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.1.2-1 [246 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.1-2 [177 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 spades amd64 3.15.5+dfsg-7 [9020 kB] Fetched 147 MB in 6s (25.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1:amd64. (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 ... 19718 files and directories currently installed.) Preparing to unpack .../libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../binfmt-support_2.2.2-7_amd64.deb ... Unpacking binfmt-support (2.2.2-7) ... Selecting previously unselected package readline-common. Preparing to unpack .../readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../libsigsegv2_2.14-1+b1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.14-1+b1) ... Setting up readline-common (8.2-4) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up libsigsegv2:amd64 (2.14-1+b1) ... Selecting previously unselected package gawk. (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 ... 19784 files and directories currently installed.) Preparing to unpack .../gawk_1%3a5.2.1-2+b1_amd64.deb ... Unpacking gawk (1:5.2.1-2+b1) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (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 ... 20288 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (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 ... 21248 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../001-libpython3.12-minimal_3.12.3-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../002-python3.12-minimal_3.12.3-1_amd64.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../003-libproc2-0_2%3a4.0.4-4_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a4.0.4-4_amd64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../006-openssl_3.2.1-3_amd64.deb ... Unpacking openssl (3.2.1-3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../007-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../008-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../009-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../010-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../011-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../012-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../013-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../014-bsdextrautils_2.40.1-1_amd64.deb ... Unpacking bsdextrautils (2.40.1-1) ... 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Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... Setting up libaom3:amd64 (3.8.2-2) ... Setting up libxau6:amd64 (1:1.0.9-1+b1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ... Setting up libjsr305-java (0.1~+svn49-11) ... Setting up bsdextrautils (2.40.1-1) ... Setting up java-common (0.75) ... Setting up libdatrie1:amd64 (0.2.13-3) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up gawk (1:5.2.1-2+b1) ... Setting up prodigal (1:2.6.3-6) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1+b1) ... Setting up bwa (0.7.17-7+b3) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libfilesys-df-perl (0.92-7+b3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpython3.12-minimal:amd64 (3.12.3-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.61.0-1+b1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libnlopt0:amd64 (2.7.1-5+b3) ... Setting up libsvtav1enc1d1:amd64 (1.7.0+dfsg-2+b1) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up librav1e0:amd64 (0.7.1-2) ... Setting up libssw-java (1.1-14+b1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libsnappy1v5:amd64 (1.2.1-1) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Jun 29 00:48:41 UTC 2025. Universal Time is now: Sun Jun 29 00:48:41 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.80.2-2) ... No schema files found: doing nothing. Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libnspr4:amd64 (2:4.35-1.1+b1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up aglfn (1.7+git20191031.4036a9c-2) ... Setting up libapache-pom-java (29-2) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up libproc2-0:amd64 (2:4.0.4-4) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up autopoint (0.21-14) ... Setting up binfmt-support (2.2.2-7) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libjsoncpp25:amd64 (1.9.5-6+b2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libpcsclite1:amd64 (2.2.2-1) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libbamtools2.5.2:amd64 (2.5.2+dfsg-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.4.0-0.1) ... Setting up dwz (0.15-1+b1) ... Setting up libdav1d7:amd64 (1.4.1-1) ... Setting up sensible-utils (0.0.22) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up bamtools (2.5.2+dfsg-5) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-4) ... Setting up mummer (3.23+dfsg-8) ... Setting up liblua5.4-0:amd64 (5.4.6-3+b1) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libabsl20230802:amd64 (20230802.1-4) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libssh2-1t64:amd64 (1.11.0-5) ... Setting up libde265-0:amd64 (1.0.15-1+b1) ... Setting up openssl (3.2.1-3) ... Setting up libwebpmux3:amd64 (1.4.0-0.1) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libyuv0:amd64 (0.0.1888.20240509-4) ... Setting up libssw0:amd64 (1.1-14+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg-2) ... 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 (1.14.0-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up gnuplot-data (6.0.0+dfsg1-3) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up libxcb1:amd64 (1.17.0-2) ... Setting up gettext (0.21-14+b1) ... Setting up libpython3.12-stdlib:amd64 (3.12.3-1) ... Setting up jarwrapper (0.79) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.17.0-2) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libedit2:amd64 (3.1-20240517-1) ... Setting up libcommons-parent-java (56-1) ... Setting up libnss3:amd64 (2:3.100-1) ... Setting up libxcb-shm0:amd64 (1.17.0-2) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libgav1-1:amd64 (0.19.0-2+b1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-4) ... Setting up libxslt1.1:amd64 (1.1.35-1+b1) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libavif16:amd64 (1.0.4-3) ... Setting up libxpm4:amd64 (1:3.5.17-1+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libcommons-compress-java (1.25.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libcurl3t64-gnutls:amd64 (8.8.0-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up python3 (3.11.8-1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up python3-packaging (24.0-1) ... Setting up python3-pluggy (1.5.0-1) ... Setting up openjdk-17-jre-headless:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up python3-lxml:amd64 (5.2.1-1) ... Setting up python3-et-xmlfile (1.0.1-2.1) ... Setting up libhts3t64:amd64 (1.19+ds-1.1+b1) ... Setting up libpangoft2-1.0-0:amd64 (1.52.2+ds-1) ... Setting up python3-lib2to3 (3.12.3-3.1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.2+ds-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-3.1) ... python3.12: can't get files for byte-compilation Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-pysam (0.22.1+ds-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-jdcal (1.0-1.3) ... Setting up python3-joblib (1.3.2-2) ... Setting up python3-pytest (8.1.2-1) ... Setting up python3-all (3.11.8-1) ... Setting up python3-yaml (6.0.1-2) ... Setting up debhelper (13.15.3) ... Setting up samtools (1.19.2-1+b1) ... Setting up python3-openpyxl (3.1.2+dfsg-6) ... Setting up spades (3.15.5+dfsg-7) ... Setting up dh-python (6.20240422) ... Setting up fastaq (3.17.0-6) ... /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s' phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s' gbk_regex = re.compile('^LOCUS\s+\S') Setting up python3-pymummer (0.11.0-4) ... Setting up libheif-plugin-dav1d:amd64 (1.17.6-1+b2) ... Setting up libheif-plugin-libde265:amd64 (1.17.6-1+b2) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libheif1:amd64 (1.17.6-1+b2) ... Setting up libguava-java (32.0.1-1) ... Setting up libgd3:amd64 (2.3.3-9+b3) ... Setting up gnuplot-nox (6.0.0+dfsg1-3) ... update-alternatives: using /usr/bin/gnuplot-nox to provide /usr/bin/gnuplot (gnuplot) in auto mode Processing triggers for libc-bin (2.38-11) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up default-jre-headless (2:1.17-75) ... Setting up jaligner (1.0+dfsg-11) ... Setting up mhap (2.1.3+dfsg-3) ... Setting up canu (2.2+dfsg-5) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... 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/reproducible-path/circlator-1.5.6/ && 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 > ../circlator_1.5.6-11_source.changes dpkg-buildpackage: info: source package circlator dpkg-buildpackage: info: source version 1.5.6-11 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py clean running clean removing '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it I: pybuild base:311: python3.11 setup.py clean running clean removing '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/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 dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config running config I: pybuild base:311: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.12 setup.py build running build running build_py creating /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator copying circlator/external_progs.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator copying circlator/mapping.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator copying circlator/common.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator copying circlator/program.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator copying circlator/versions.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator copying circlator/clean.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator copying circlator/bamfilter.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator copying circlator/assemble.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator copying circlator/minimus2.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator copying circlator/__init__.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator copying circlator/dnaa.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator copying circlator/merge.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator copying circlator/start_fixer.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator copying circlator/assembly.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator creating /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks copying circlator/tasks/all.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks copying circlator/tasks/version.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks copying circlator/tasks/progcheck.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks copying circlator/tasks/clean.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks copying circlator/tasks/test.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks copying circlator/tasks/fixstart.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks copying circlator/tasks/assemble.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks copying circlator/tasks/mapreads.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks copying circlator/tasks/bam2reads.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks copying circlator/tasks/minimus2.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks copying circlator/tasks/__init__.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks copying circlator/tasks/merge.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks copying circlator/tasks/get_dnaa.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks creating /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/data copying circlator/data/dnaA.fasta -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/data copying circlator/data/test_make_data.sh -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/data copying circlator/data/test_for_reads.fa -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/data copying circlator/data/test_reads.fq.gz -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/data copying circlator/data/test_ref.fa -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/data copying circlator/data/test_ref.fa.fai -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/data copying circlator/data/test_contigs.fa -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/data running build_scripts creating build creating build/scripts-3.12 copying and adjusting scripts/circlator -> build/scripts-3.12 changing mode of build/scripts-3.12/circlator from 644 to 755 I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator copying circlator/external_progs.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator copying circlator/mapping.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator copying circlator/common.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator copying circlator/program.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator copying circlator/versions.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator copying circlator/clean.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator copying circlator/bamfilter.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator copying circlator/assemble.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator copying circlator/minimus2.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator copying circlator/__init__.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator copying circlator/dnaa.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator copying circlator/merge.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator copying circlator/start_fixer.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator copying circlator/assembly.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator creating /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks copying circlator/tasks/all.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks copying circlator/tasks/version.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks copying circlator/tasks/progcheck.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks copying circlator/tasks/clean.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks copying circlator/tasks/test.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks copying circlator/tasks/fixstart.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks copying circlator/tasks/assemble.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks copying circlator/tasks/mapreads.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks copying circlator/tasks/bam2reads.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks copying circlator/tasks/minimus2.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks copying circlator/tasks/__init__.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks copying circlator/tasks/merge.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks copying circlator/tasks/get_dnaa.py -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks creating /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/data copying circlator/data/dnaA.fasta -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/data copying circlator/data/test_make_data.sh -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/data copying circlator/data/test_for_reads.fa -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/data copying circlator/data/test_reads.fq.gz -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/data copying circlator/data/test_ref.fa -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/data copying circlator/data/test_ref.fa.fai -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/data copying circlator/data/test_contigs.fa -> /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/data running build_scripts creating build/scripts-3.11 copying and adjusting scripts/circlator -> build/scripts-3.11 changing mode of build/scripts-3.11/circlator from 644 to 755 dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: cp -av circlator/tests /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/ 'circlator/tests' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests' 'circlator/tests/assembly_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/assembly_test.py' 'circlator/tests/bamfilter_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/bamfilter_test.py' 'circlator/tests/clean_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/clean_test.py' 'circlator/tests/common_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/common_test.py' 'circlator/tests/data' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data' 'circlator/tests/data/assemble_test.dummy_reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assemble_test.dummy_reads.fa' 'circlator/tests/data/assemble_test_rename_canu_contigs.expect.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assemble_test_rename_canu_contigs.expect.fa' 'circlator/tests/data/assemble_test_rename_canu_contigs.in.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assemble_test_rename_canu_contigs.in.fa' 'circlator/tests/data/assembly_test_circular_contigs_from_canu.gfa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_from_canu.gfa' 'circlator/tests/data/assembly_test_circular_contigs_from_spades_after_3_6_1.assembly_graph.fastg' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_from_spades_after_3_6_1.assembly_graph.fastg' 'circlator/tests/data/assembly_test_circular_contigs_from_spades_after_3_6_1.contigs.paths' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_from_spades_after_3_6_1.contigs.paths' 'circlator/tests/data/assembly_test_circular_contigs_from_spades_before_3_6_1.fastg' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_from_spades_before_3_6_1.fastg' 'circlator/tests/data/assembly_test_circular_contigs_only_contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_only_contigs.fasta' 'circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1' 'circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/assembly_graph.fastg' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/assembly_graph.fastg' 'circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/contigs.fasta' 'circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/contigs.paths' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/contigs.paths' 'circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1' 'circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1/contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1/contigs.fasta' 'circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1/contigs.fastg' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1/contigs.fastg' 'circlator/tests/data/assembly_test_get_contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_get_contigs.fasta' 'circlator/tests/data/assembly_test_init_contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_contigs.fasta' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph/contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph/contigs.fasta' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph/contigs.paths' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph/contigs.paths' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph_or_contig_paths' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph_or_contig_paths' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph_or_contig_paths/contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph_or_contig_paths/contigs.fasta' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths/assembly_graph.fastg' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths/assembly_graph.fastg' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths/contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths/contigs.fasta' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/assembly_graph.fastg' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/assembly_graph.fastg' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/contigs.fasta' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/contigs.paths' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/contigs.paths' 'circlator/tests/data/assembly_test_init_spades_pre_3_6_1_no_fastg' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_no_fastg' 'circlator/tests/data/assembly_test_init_spades_pre_3_6_1_no_fastg/contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_no_fastg/contigs.fasta' 'circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok' 'circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok/contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok/contigs.fasta' 'circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok/contigs.fastg' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok/contigs.fastg' 'circlator/tests/data/assembly_test_spades_contigs_paths_to_dict.contigs.paths' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_spades_contigs_paths_to_dict.contigs.paths' 'circlator/tests/data/bamfilter_test_all_reads_from_contig.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_all_reads_from_contig.bam' 'circlator/tests/data/bamfilter_test_all_reads_from_contig.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_all_reads_from_contig.bam.bai' 'circlator/tests/data/bamfilter_test_all_reads_from_contig.reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_all_reads_from_contig.reads.fa' 'circlator/tests/data/bamfilter_test_all_reads_from_contig.reads.fq' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_all_reads_from_contig.reads.fq' 'circlator/tests/data/bamfilter_test_break_reads.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_break_reads.bam' 'circlator/tests/data/bamfilter_test_break_reads.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_break_reads.bam.bai' 'circlator/tests/data/bamfilter_test_break_reads.broken_reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_break_reads.broken_reads.fa' 'circlator/tests/data/bamfilter_test_break_reads.broken_reads.fq' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_break_reads.broken_reads.fq' 'circlator/tests/data/bamfilter_test_check_contigs_to_use.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_check_contigs_to_use.bam' 'circlator/tests/data/bamfilter_test_check_contigs_to_use.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_check_contigs_to_use.bam.bai' 'circlator/tests/data/bamfilter_test_exclude_region.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_exclude_region.bam' 'circlator/tests/data/bamfilter_test_exclude_region.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_exclude_region.bam.bai' 'circlator/tests/data/bamfilter_test_exclude_region.reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_exclude_region.reads.fa' 'circlator/tests/data/bamfilter_test_exclude_region.reads.fq' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_exclude_region.reads.fq' 'circlator/tests/data/bamfilter_test_get_all_unmapped_reads.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.bam' 'circlator/tests/data/bamfilter_test_get_all_unmapped_reads.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.bam.bai' 'circlator/tests/data/bamfilter_test_get_all_unmapped_reads.reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.reads.fa' 'circlator/tests/data/bamfilter_test_get_all_unmapped_reads.reads.fq' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.reads.fq' 'circlator/tests/data/bamfilter_test_get_contigs_to_use.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_contigs_to_use.bam' 'circlator/tests/data/bamfilter_test_get_contigs_to_use.infile' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_contigs_to_use.infile' 'circlator/tests/data/bamfilter_test_get_ref_lengths.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_ref_lengths.bam' 'circlator/tests/data/bamfilter_test_get_region_end.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_region_end.bam' 'circlator/tests/data/bamfilter_test_get_region_end.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_region_end.bam.bai' 'circlator/tests/data/bamfilter_test_get_region_end.reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_region_end.reads.fa' 'circlator/tests/data/bamfilter_test_get_region_start.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_region_start.bam' 'circlator/tests/data/bamfilter_test_get_region_start.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_region_start.bam.bai' 'circlator/tests/data/bamfilter_test_get_region_start.reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_region_start.reads.fa' 'circlator/tests/data/bamfilter_test_run.make_reads_and_bam.sh' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run.make_reads_and_bam.sh' 'circlator/tests/data/bamfilter_test_run.reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run.reads.fa' 'circlator/tests/data/bamfilter_test_run.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run.ref.fa' 'circlator/tests/data/bamfilter_test_run.ref.fa.fai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run.ref.fa.fai' 'circlator/tests/data/bamfilter_test_run_discard_unmapped.out.reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run_discard_unmapped.out.reads.fa' 'circlator/tests/data/bamfilter_test_run_keep_unmapped.out.reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run_keep_unmapped.out.reads.fa' 'circlator/tests/data/bamfilter_test_run_keep_unmapped.out.reads.fq' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run_keep_unmapped.out.reads.fq' 'circlator/tests/data/bamfilter_test_run_no_qual.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run_no_qual.bam' 'circlator/tests/data/bamfilter_test_run_no_qual.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run_no_qual.bam.bai' 'circlator/tests/data/bamfilter_test_run_with_qual.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run_with_qual.bam' 'circlator/tests/data/bamfilter_test_run_with_qual.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run_with_qual.bam.bai' 'circlator/tests/data/clean_test_clean_contigs.in.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/clean_test_clean_contigs.in.fa' 'circlator/tests/data/clean_test_clean_contigs.out.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/clean_test_clean_contigs.out.fa' 'circlator/tests/data/clean_test_contigs_to_keep' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/clean_test_contigs_to_keep' 'circlator/tests/data/clean_test_load_nucmer_hits.coords' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/clean_test_load_nucmer_hits.coords' 'circlator/tests/data/clean_test_remove_small_contigs.in.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/clean_test_remove_small_contigs.in.fa' 'circlator/tests/data/clean_test_remove_small_contigs.out.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/clean_test_remove_small_contigs.out.fa' 'circlator/tests/data/clean_test_write_log.log' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/clean_test_write_log.log' 'circlator/tests/data/common_test_file_exists' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/common_test_file_exists' 'circlator/tests/data/mapping_test_aligned_read_to_read.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/mapping_test_aligned_read_to_read.bam' 'circlator/tests/data/mapping_test_aligned_read_to_read.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/mapping_test_aligned_read_to_read.bam.bai' 'circlator/tests/data/mapping_test_aligned_read_to_read.reads.fq' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/mapping_test_aligned_read_to_read.reads.fq' 'circlator/tests/data/mapping_test_aligned_read_to_read.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/mapping_test_aligned_read_to_read.ref.fa' 'circlator/tests/data/mapping_test_bwa_index.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/mapping_test_bwa_index.fa' 'circlator/tests/data/mapping_test_bwa_mem.reads.fq' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/mapping_test_bwa_mem.reads.fq' 'circlator/tests/data/mapping_test_bwa_mem.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/mapping_test_bwa_mem.ref.fa' 'circlator/tests/data/mapping_test_bwa_mem.ref.fa.fai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/mapping_test_bwa_mem.ref.fa.fai' 'circlator/tests/data/merge_test_contigs_dict_to_file.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_contigs_dict_to_file.fa' 'circlator/tests/data/merge_test_get_spades_circular_nodes.fastg' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_get_spades_circular_nodes.fastg' 'circlator/tests/data/merge_test_hits_to_new_seq.1.expected.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_hits_to_new_seq.1.expected.fa' 'circlator/tests/data/merge_test_hits_to_new_seq.1.reassembly.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_hits_to_new_seq.1.reassembly.fa' 'circlator/tests/data/merge_test_hits_to_new_seq.1.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_hits_to_new_seq.1.ref.fa' 'circlator/tests/data/merge_test_hits_to_new_seq.2.expected.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_hits_to_new_seq.2.expected.fa' 'circlator/tests/data/merge_test_hits_to_new_seq.2.reassembly.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_hits_to_new_seq.2.reassembly.fa' 'circlator/tests/data/merge_test_hits_to_new_seq.2.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_hits_to_new_seq.2.ref.fa' 'circlator/tests/data/merge_test_index_fasta.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_index_fasta.fa' 'circlator/tests/data/merge_test_index_fasta.fa.fai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_index_fasta.fa.fai' 'circlator/tests/data/merge_test_load_nucmer_hits.coords' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_load_nucmer_hits.coords' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.expected.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.expected.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.reassembly.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.reassembly.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.ref.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.expected.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.expected.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.reassembly.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.reassembly.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.ref.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.expected.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.expected.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.reassembly.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.reassembly.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.ref.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.expected.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.expected.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.reassembly.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.reassembly.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.ref.fa' 'circlator/tests/data/merge_test_merge_pair.test1.coords' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_pair.test1.coords' 'circlator/tests/data/merge_test_merge_pair.test2.coords' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_pair.test2.coords' 'circlator/tests/data/merge_test_merge_pair.test3.coords' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_pair.test3.coords' 'circlator/tests/data/merge_test_nucmer_hits_to_potential_join.reassembly.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_nucmer_hits_to_potential_join.reassembly.fa' 'circlator/tests/data/merge_test_nucmer_hits_to_potential_join.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_nucmer_hits_to_potential_join.ref.fa' 'circlator/tests/data/merge_test_original.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_original.fa' 'circlator/tests/data/merge_test_reassembly.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_reassembly.fa' 'circlator/tests/data/merge_test_write_act_files.coords' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_write_act_files.coords' 'circlator/tests/data/merge_test_write_act_files.expected.crunch' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_write_act_files.expected.crunch' 'circlator/tests/data/merge_test_write_act_files.expected.sh' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_write_act_files.expected.sh' 'circlator/tests/data/merge_test_write_act_files.qry.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_write_act_files.qry.fa' 'circlator/tests/data/merge_test_write_act_files.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_write_act_files.ref.fa' 'circlator/tests/data/minimus2_test.dummy_input_assembly.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test.dummy_input_assembly.fa' 'circlator/tests/data/minimus2_test.write_split_contig.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test.write_split_contig.fa' 'circlator/tests/data/minimus2_test_run_initial_merge.expected.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test_run_initial_merge.expected.fa' 'circlator/tests/data/minimus2_test_run_initial_merge.in.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test_run_initial_merge.in.fa' 'circlator/tests/data/minimus2_test_run_minimus2.in.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test_run_minimus2.in.fa' 'circlator/tests/data/minimus2_test_run_minimus2_on_each_contig.expected.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test_run_minimus2_on_each_contig.expected.fa' 'circlator/tests/data/minimus2_test_run_minimus2_on_each_contig.in.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test_run_minimus2_on_each_contig.in.fa' 'circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.expected.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.expected.fa' 'circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.fa' 'circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.in.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.in.fa' 'circlator/tests/data/start_fixer_find_circular_using_prodigal.ctgs.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_find_circular_using_prodigal.ctgs.fa' 'circlator/tests/data/start_fixer_find_circular_using_promer.contigs.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_find_circular_using_promer.contigs.fa' 'circlator/tests/data/start_fixer_find_circular_using_promer.refs.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_find_circular_using_promer.refs.fa' 'circlator/tests/data/start_fixer_init_contigs.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_init_contigs.fa' 'circlator/tests/data/start_fixer_init_dnaA.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_init_dnaA.fa' 'circlator/tests/data/start_fixer_init_ignore_ids' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_init_ignore_ids' 'circlator/tests/data/start_fixer_max_length_from_fasta_file.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_max_length_from_fasta_file.fa' 'circlator/tests/data/start_fixer_rearrange_contigs.expect.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_rearrange_contigs.expect.fa' 'circlator/tests/data/start_fixer_rearrange_contigs.expect.log' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_rearrange_contigs.expect.log' 'circlator/tests/data/start_fixer_rearrange_contigs.in.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_rearrange_contigs.in.fa' 'circlator/tests/data/start_fixer_rearrange_contigs.refs.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_rearrange_contigs.refs.fa' 'circlator/tests/data/start_fixer_run_bit_of_everything.ctg.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_bit_of_everything.ctg.fa' 'circlator/tests/data/start_fixer_run_bit_of_everything.expect.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_bit_of_everything.expect.fa' 'circlator/tests/data/start_fixer_run_bit_of_everything.ignore' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_bit_of_everything.ignore' 'circlator/tests/data/start_fixer_run_bit_of_everything.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_bit_of_everything.ref.fa' 'circlator/tests/data/start_fixer_run_ignore_all.expect.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_ignore_all.expect.fa' 'circlator/tests/data/start_fixer_run_ignore_all.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_ignore_all.fa' 'circlator/tests/data/start_fixer_run_ignore_all.to_ignore' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_ignore_all.to_ignore' 'circlator/tests/data/start_fixer_run_none_for_prodigal.ctg.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_none_for_prodigal.ctg.fa' 'circlator/tests/data/start_fixer_run_none_for_prodigal.expect.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_none_for_prodigal.expect.fa' 'circlator/tests/data/start_fixer_run_none_for_prodigal.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_none_for_prodigal.ref.fa' 'circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.in.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.in.fa' 'circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.fa' 'circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.ignore.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.ignore.fa' 'circlator/tests/data/start_fixer_write_renamed_contigs.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_write_renamed_contigs.fa' 'circlator/tests/dnaa_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/dnaa_test.py' 'circlator/tests/external_progs_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/external_progs_test.py' 'circlator/tests/mapping_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/mapping_test.py' 'circlator/tests/merge_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/merge_test.py' 'circlator/tests/minimus2_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/minimus2_test.py' 'circlator/tests/start_fixer_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/start_fixer_test.py' 'circlator/tests/assemble_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/assemble_test.py' I: pybuild base:311: cd /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build; python3.12 -m pytest circlator/tests ============================= test session starts ============================== platform linux -- Python 3.12.3, pytest-8.1.2, pluggy-1.5.0 rootdir: /build/reproducible-path/circlator-1.5.6 collected 115 items circlator/tests/assemble_test.py .... [ 3%] circlator/tests/assembly_test.py ............. [ 14%] circlator/tests/bamfilter_test.py ............ [ 25%] circlator/tests/clean_test.py ............... [ 38%] circlator/tests/common_test.py . [ 39%] circlator/tests/dnaa_test.py ...... [ 44%] circlator/tests/external_progs_test.py ....... [ 50%] circlator/tests/mapping_test.py .... [ 53%] circlator/tests/merge_test.py .................................... [ 85%] circlator/tests/minimus2_test.py ssssss [ 90%] circlator/tests/start_fixer_test.py ........... [100%] =============================== warnings summary =============================== ../../../../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:1 /usr/lib/python3/dist-packages/pyfastaq/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import get_distribution circlator/dnaa.py:18 /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/dnaa.py:18: SyntaxWarning: invalid escape sequence '\s' self.uniprot_search = re.sub('\s+', '+', uniprot_search.strip()) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ================== 109 passed, 6 skipped, 2 warnings in 2.54s ================== I: pybuild pybuild:308: cp -av circlator/tests /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/ 'circlator/tests' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests' 'circlator/tests/assembly_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/assembly_test.py' 'circlator/tests/bamfilter_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/bamfilter_test.py' 'circlator/tests/clean_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/clean_test.py' 'circlator/tests/common_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/common_test.py' 'circlator/tests/data' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data' 'circlator/tests/data/assemble_test.dummy_reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assemble_test.dummy_reads.fa' 'circlator/tests/data/assemble_test_rename_canu_contigs.expect.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assemble_test_rename_canu_contigs.expect.fa' 'circlator/tests/data/assemble_test_rename_canu_contigs.in.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assemble_test_rename_canu_contigs.in.fa' 'circlator/tests/data/assembly_test_circular_contigs_from_canu.gfa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_from_canu.gfa' 'circlator/tests/data/assembly_test_circular_contigs_from_spades_after_3_6_1.assembly_graph.fastg' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_from_spades_after_3_6_1.assembly_graph.fastg' 'circlator/tests/data/assembly_test_circular_contigs_from_spades_after_3_6_1.contigs.paths' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_from_spades_after_3_6_1.contigs.paths' 'circlator/tests/data/assembly_test_circular_contigs_from_spades_before_3_6_1.fastg' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_from_spades_before_3_6_1.fastg' 'circlator/tests/data/assembly_test_circular_contigs_only_contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_only_contigs.fasta' 'circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1' 'circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/assembly_graph.fastg' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/assembly_graph.fastg' 'circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/contigs.fasta' 'circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/contigs.paths' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/contigs.paths' 'circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1' 'circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1/contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1/contigs.fasta' 'circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1/contigs.fastg' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1/contigs.fastg' 'circlator/tests/data/assembly_test_get_contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_get_contigs.fasta' 'circlator/tests/data/assembly_test_init_contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_contigs.fasta' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph/contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph/contigs.fasta' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph/contigs.paths' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph/contigs.paths' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph_or_contig_paths' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph_or_contig_paths' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph_or_contig_paths/contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph_or_contig_paths/contigs.fasta' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths/assembly_graph.fastg' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths/assembly_graph.fastg' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths/contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths/contigs.fasta' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/assembly_graph.fastg' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/assembly_graph.fastg' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/contigs.fasta' 'circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/contigs.paths' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/contigs.paths' 'circlator/tests/data/assembly_test_init_spades_pre_3_6_1_no_fastg' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_no_fastg' 'circlator/tests/data/assembly_test_init_spades_pre_3_6_1_no_fastg/contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_no_fastg/contigs.fasta' 'circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok' 'circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok/contigs.fasta' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok/contigs.fasta' 'circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok/contigs.fastg' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok/contigs.fastg' 'circlator/tests/data/assembly_test_spades_contigs_paths_to_dict.contigs.paths' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_spades_contigs_paths_to_dict.contigs.paths' 'circlator/tests/data/bamfilter_test_all_reads_from_contig.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_all_reads_from_contig.bam' 'circlator/tests/data/bamfilter_test_all_reads_from_contig.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_all_reads_from_contig.bam.bai' 'circlator/tests/data/bamfilter_test_all_reads_from_contig.reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_all_reads_from_contig.reads.fa' 'circlator/tests/data/bamfilter_test_all_reads_from_contig.reads.fq' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_all_reads_from_contig.reads.fq' 'circlator/tests/data/bamfilter_test_break_reads.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_break_reads.bam' 'circlator/tests/data/bamfilter_test_break_reads.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_break_reads.bam.bai' 'circlator/tests/data/bamfilter_test_break_reads.broken_reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_break_reads.broken_reads.fa' 'circlator/tests/data/bamfilter_test_break_reads.broken_reads.fq' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_break_reads.broken_reads.fq' 'circlator/tests/data/bamfilter_test_check_contigs_to_use.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_check_contigs_to_use.bam' 'circlator/tests/data/bamfilter_test_check_contigs_to_use.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_check_contigs_to_use.bam.bai' 'circlator/tests/data/bamfilter_test_exclude_region.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_exclude_region.bam' 'circlator/tests/data/bamfilter_test_exclude_region.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_exclude_region.bam.bai' 'circlator/tests/data/bamfilter_test_exclude_region.reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_exclude_region.reads.fa' 'circlator/tests/data/bamfilter_test_exclude_region.reads.fq' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_exclude_region.reads.fq' 'circlator/tests/data/bamfilter_test_get_all_unmapped_reads.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.bam' 'circlator/tests/data/bamfilter_test_get_all_unmapped_reads.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.bam.bai' 'circlator/tests/data/bamfilter_test_get_all_unmapped_reads.reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.reads.fa' 'circlator/tests/data/bamfilter_test_get_all_unmapped_reads.reads.fq' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.reads.fq' 'circlator/tests/data/bamfilter_test_get_contigs_to_use.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_contigs_to_use.bam' 'circlator/tests/data/bamfilter_test_get_contigs_to_use.infile' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_contigs_to_use.infile' 'circlator/tests/data/bamfilter_test_get_ref_lengths.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_ref_lengths.bam' 'circlator/tests/data/bamfilter_test_get_region_end.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_region_end.bam' 'circlator/tests/data/bamfilter_test_get_region_end.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_region_end.bam.bai' 'circlator/tests/data/bamfilter_test_get_region_end.reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_region_end.reads.fa' 'circlator/tests/data/bamfilter_test_get_region_start.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_region_start.bam' 'circlator/tests/data/bamfilter_test_get_region_start.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_region_start.bam.bai' 'circlator/tests/data/bamfilter_test_get_region_start.reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_region_start.reads.fa' 'circlator/tests/data/bamfilter_test_run.make_reads_and_bam.sh' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run.make_reads_and_bam.sh' 'circlator/tests/data/bamfilter_test_run.reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run.reads.fa' 'circlator/tests/data/bamfilter_test_run.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run.ref.fa' 'circlator/tests/data/bamfilter_test_run.ref.fa.fai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run.ref.fa.fai' 'circlator/tests/data/bamfilter_test_run_discard_unmapped.out.reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run_discard_unmapped.out.reads.fa' 'circlator/tests/data/bamfilter_test_run_keep_unmapped.out.reads.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run_keep_unmapped.out.reads.fa' 'circlator/tests/data/bamfilter_test_run_keep_unmapped.out.reads.fq' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run_keep_unmapped.out.reads.fq' 'circlator/tests/data/bamfilter_test_run_no_qual.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run_no_qual.bam' 'circlator/tests/data/bamfilter_test_run_no_qual.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run_no_qual.bam.bai' 'circlator/tests/data/bamfilter_test_run_with_qual.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run_with_qual.bam' 'circlator/tests/data/bamfilter_test_run_with_qual.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run_with_qual.bam.bai' 'circlator/tests/data/clean_test_clean_contigs.in.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/clean_test_clean_contigs.in.fa' 'circlator/tests/data/clean_test_clean_contigs.out.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/clean_test_clean_contigs.out.fa' 'circlator/tests/data/clean_test_contigs_to_keep' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/clean_test_contigs_to_keep' 'circlator/tests/data/clean_test_load_nucmer_hits.coords' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/clean_test_load_nucmer_hits.coords' 'circlator/tests/data/clean_test_remove_small_contigs.in.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/clean_test_remove_small_contigs.in.fa' 'circlator/tests/data/clean_test_remove_small_contigs.out.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/clean_test_remove_small_contigs.out.fa' 'circlator/tests/data/clean_test_write_log.log' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/clean_test_write_log.log' 'circlator/tests/data/common_test_file_exists' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/common_test_file_exists' 'circlator/tests/data/mapping_test_aligned_read_to_read.bam' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/mapping_test_aligned_read_to_read.bam' 'circlator/tests/data/mapping_test_aligned_read_to_read.bam.bai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/mapping_test_aligned_read_to_read.bam.bai' 'circlator/tests/data/mapping_test_aligned_read_to_read.reads.fq' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/mapping_test_aligned_read_to_read.reads.fq' 'circlator/tests/data/mapping_test_aligned_read_to_read.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/mapping_test_aligned_read_to_read.ref.fa' 'circlator/tests/data/mapping_test_bwa_index.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/mapping_test_bwa_index.fa' 'circlator/tests/data/mapping_test_bwa_mem.reads.fq' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/mapping_test_bwa_mem.reads.fq' 'circlator/tests/data/mapping_test_bwa_mem.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/mapping_test_bwa_mem.ref.fa' 'circlator/tests/data/mapping_test_bwa_mem.ref.fa.fai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/mapping_test_bwa_mem.ref.fa.fai' 'circlator/tests/data/merge_test_contigs_dict_to_file.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_contigs_dict_to_file.fa' 'circlator/tests/data/merge_test_get_spades_circular_nodes.fastg' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_get_spades_circular_nodes.fastg' 'circlator/tests/data/merge_test_hits_to_new_seq.1.expected.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_hits_to_new_seq.1.expected.fa' 'circlator/tests/data/merge_test_hits_to_new_seq.1.reassembly.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_hits_to_new_seq.1.reassembly.fa' 'circlator/tests/data/merge_test_hits_to_new_seq.1.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_hits_to_new_seq.1.ref.fa' 'circlator/tests/data/merge_test_hits_to_new_seq.2.expected.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_hits_to_new_seq.2.expected.fa' 'circlator/tests/data/merge_test_hits_to_new_seq.2.reassembly.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_hits_to_new_seq.2.reassembly.fa' 'circlator/tests/data/merge_test_hits_to_new_seq.2.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_hits_to_new_seq.2.ref.fa' 'circlator/tests/data/merge_test_index_fasta.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_index_fasta.fa' 'circlator/tests/data/merge_test_index_fasta.fa.fai' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_index_fasta.fa.fai' 'circlator/tests/data/merge_test_load_nucmer_hits.coords' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_load_nucmer_hits.coords' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.expected.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.expected.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.reassembly.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.reassembly.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.ref.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.expected.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.expected.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.reassembly.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.reassembly.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.ref.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.expected.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.expected.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.reassembly.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.reassembly.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.ref.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.expected.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.expected.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.reassembly.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.reassembly.fa' 'circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.ref.fa' 'circlator/tests/data/merge_test_merge_pair.test1.coords' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_pair.test1.coords' 'circlator/tests/data/merge_test_merge_pair.test2.coords' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_pair.test2.coords' 'circlator/tests/data/merge_test_merge_pair.test3.coords' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_pair.test3.coords' 'circlator/tests/data/merge_test_nucmer_hits_to_potential_join.reassembly.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_nucmer_hits_to_potential_join.reassembly.fa' 'circlator/tests/data/merge_test_nucmer_hits_to_potential_join.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_nucmer_hits_to_potential_join.ref.fa' 'circlator/tests/data/merge_test_original.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_original.fa' 'circlator/tests/data/merge_test_reassembly.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_reassembly.fa' 'circlator/tests/data/merge_test_write_act_files.coords' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_write_act_files.coords' 'circlator/tests/data/merge_test_write_act_files.expected.crunch' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_write_act_files.expected.crunch' 'circlator/tests/data/merge_test_write_act_files.expected.sh' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_write_act_files.expected.sh' 'circlator/tests/data/merge_test_write_act_files.qry.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_write_act_files.qry.fa' 'circlator/tests/data/merge_test_write_act_files.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_write_act_files.ref.fa' 'circlator/tests/data/minimus2_test.dummy_input_assembly.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test.dummy_input_assembly.fa' 'circlator/tests/data/minimus2_test.write_split_contig.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test.write_split_contig.fa' 'circlator/tests/data/minimus2_test_run_initial_merge.expected.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test_run_initial_merge.expected.fa' 'circlator/tests/data/minimus2_test_run_initial_merge.in.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test_run_initial_merge.in.fa' 'circlator/tests/data/minimus2_test_run_minimus2.in.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test_run_minimus2.in.fa' 'circlator/tests/data/minimus2_test_run_minimus2_on_each_contig.expected.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test_run_minimus2_on_each_contig.expected.fa' 'circlator/tests/data/minimus2_test_run_minimus2_on_each_contig.in.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test_run_minimus2_on_each_contig.in.fa' 'circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.expected.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.expected.fa' 'circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.fa' 'circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.in.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.in.fa' 'circlator/tests/data/start_fixer_find_circular_using_prodigal.ctgs.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_find_circular_using_prodigal.ctgs.fa' 'circlator/tests/data/start_fixer_find_circular_using_promer.contigs.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_find_circular_using_promer.contigs.fa' 'circlator/tests/data/start_fixer_find_circular_using_promer.refs.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_find_circular_using_promer.refs.fa' 'circlator/tests/data/start_fixer_init_contigs.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_init_contigs.fa' 'circlator/tests/data/start_fixer_init_dnaA.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_init_dnaA.fa' 'circlator/tests/data/start_fixer_init_ignore_ids' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_init_ignore_ids' 'circlator/tests/data/start_fixer_max_length_from_fasta_file.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_max_length_from_fasta_file.fa' 'circlator/tests/data/start_fixer_rearrange_contigs.expect.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_rearrange_contigs.expect.fa' 'circlator/tests/data/start_fixer_rearrange_contigs.expect.log' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_rearrange_contigs.expect.log' 'circlator/tests/data/start_fixer_rearrange_contigs.in.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_rearrange_contigs.in.fa' 'circlator/tests/data/start_fixer_rearrange_contigs.refs.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_rearrange_contigs.refs.fa' 'circlator/tests/data/start_fixer_run_bit_of_everything.ctg.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_bit_of_everything.ctg.fa' 'circlator/tests/data/start_fixer_run_bit_of_everything.expect.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_bit_of_everything.expect.fa' 'circlator/tests/data/start_fixer_run_bit_of_everything.ignore' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_bit_of_everything.ignore' 'circlator/tests/data/start_fixer_run_bit_of_everything.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_bit_of_everything.ref.fa' 'circlator/tests/data/start_fixer_run_ignore_all.expect.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_ignore_all.expect.fa' 'circlator/tests/data/start_fixer_run_ignore_all.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_ignore_all.fa' 'circlator/tests/data/start_fixer_run_ignore_all.to_ignore' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_ignore_all.to_ignore' 'circlator/tests/data/start_fixer_run_none_for_prodigal.ctg.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_none_for_prodigal.ctg.fa' 'circlator/tests/data/start_fixer_run_none_for_prodigal.expect.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_none_for_prodigal.expect.fa' 'circlator/tests/data/start_fixer_run_none_for_prodigal.ref.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_none_for_prodigal.ref.fa' 'circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.in.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.in.fa' 'circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.fa' 'circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.ignore.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.ignore.fa' 'circlator/tests/data/start_fixer_write_renamed_contigs.fa' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_write_renamed_contigs.fa' 'circlator/tests/dnaa_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/dnaa_test.py' 'circlator/tests/external_progs_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/external_progs_test.py' 'circlator/tests/mapping_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/mapping_test.py' 'circlator/tests/merge_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/merge_test.py' 'circlator/tests/minimus2_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/minimus2_test.py' 'circlator/tests/start_fixer_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/start_fixer_test.py' 'circlator/tests/assemble_test.py' -> '/build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/assemble_test.py' I: pybuild base:311: cd /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build; python3.11 -m pytest circlator/tests ============================= test session starts ============================== platform linux -- Python 3.11.9, pytest-8.1.2, pluggy-1.5.0 rootdir: /build/reproducible-path/circlator-1.5.6 collected 115 items circlator/tests/assemble_test.py .... [ 3%] circlator/tests/assembly_test.py ............. [ 14%] circlator/tests/bamfilter_test.py ............ [ 25%] circlator/tests/clean_test.py ............... [ 38%] circlator/tests/common_test.py . [ 39%] circlator/tests/dnaa_test.py ...... [ 44%] circlator/tests/external_progs_test.py ....... [ 50%] circlator/tests/mapping_test.py .... [ 53%] circlator/tests/merge_test.py .................................... [ 85%] circlator/tests/minimus2_test.py ssssss [ 90%] circlator/tests/start_fixer_test.py ........... [100%] =============================== warnings summary =============================== ../../../../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:1 /usr/lib/python3/dist-packages/pyfastaq/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import get_distribution circlator/dnaa.py:18 /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/dnaa.py:18: DeprecationWarning: invalid escape sequence '\s' self.uniprot_search = re.sub('\s+', '+', uniprot_search.strip()) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ================== 109 passed, 6 skipped, 2 warnings in 1.54s ================== create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/circlator/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.12 setup.py install --root /build/reproducible-path/circlator-1.5.6/debian/circlator running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_scripts running install_lib creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12 creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/external_progs.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/mapping.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/common.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/program.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/start_fixer_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/merge_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/__pycache__/common_test.cpython-312-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/__pycache__/bamfilter_test.cpython-312-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/__pycache__/external_progs_test.cpython-312-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/__pycache__/minimus2_test.cpython-312-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/__pycache__/start_fixer_test.cpython-312-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/__pycache__/mapping_test.cpython-312-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/__pycache__/clean_test.cpython-312-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/__pycache__/merge_test.cpython-312-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/__pycache__/assemble_test.cpython-312-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/__pycache__/dnaa_test.cpython-312-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/__pycache__/assembly_test.cpython-312-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/__pycache__ creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_nucmer_hits_to_potential_join.reassembly.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_find_circular_using_promer.contigs.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test.dummy_input_assembly.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_nucmer_hits_to_potential_join.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_from_spades_after_3_6_1.assembly_graph.fastg -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_rearrange_contigs.in.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/mapping_test_aligned_read_to_read.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_write_act_files.expected.sh -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_from_canu.gfa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_init_dnaA.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_no_fastg copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_no_fastg/contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_no_fastg copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_rearrange_contigs.expect.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test_run_initial_merge.in.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_region_end.reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok/contigs.fastg -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok/contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_all_reads_from_contig.reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_exclude_region.reads.fq -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.reassembly.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run.reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_rearrange_contigs.expect.log -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_all_reads_from_contig.reads.fq -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.expected.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run.ref.fa.fai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/mapping_test_aligned_read_to_read.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assemble_test.dummy_reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_exclude_region.reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.reads.fq -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_only_contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_hits_to_new_seq.1.expected.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test_run_minimus2_on_each_contig.expected.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_bit_of_everything.ctg.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/mapping_test_bwa_mem.ref.fa.fai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_region_end.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_ref_lengths.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_init_contigs.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/clean_test_remove_small_contigs.out.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run_discard_unmapped.out.reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_ignore_all.to_ignore -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph/contigs.paths -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph/contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_original.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.in.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test_run_minimus2_on_each_contig.in.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.reassembly.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_pair.test2.coords -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/mapping_test_bwa_index.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_write_act_files.coords -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_find_circular_using_promer.refs.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_spades_contigs_paths_to_dict.contigs.paths -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_check_contigs_to_use.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_all_reads_from_contig.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assemble_test_rename_canu_contigs.expect.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/mapping_test_aligned_read_to_read.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/contigs.paths -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/assembly_graph.fastg -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/clean_test_contigs_to_keep -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.ignore.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/common_test_file_exists -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.reassembly.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.expected.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/clean_test_clean_contigs.in.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/mapping_test_bwa_mem.reads.fq -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_from_spades_after_3_6_1.contigs.paths -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run_no_qual.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_get_spades_circular_nodes.fastg -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_region_start.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1 copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1/contigs.fastg -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1 copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1/contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1 copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_all_reads_from_contig.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_index_fasta.fa.fai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_region_start.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_hits_to_new_seq.1.reassembly.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_contigs_dict_to_file.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run_with_qual.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_contigs_to_use.infile -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_break_reads.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_break_reads.broken_reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test_run_minimus2.in.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/clean_test_clean_contigs.out.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_write_renamed_contigs.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_from_spades_before_3_6_1.fastg -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/clean_test_load_nucmer_hits.coords -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_contigs_to_use.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.in.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/clean_test_remove_small_contigs.in.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/mapping_test_aligned_read_to_read.reads.fq -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_reassembly.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/mapping_test_bwa_mem.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_hits_to_new_seq.2.reassembly.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test.write_split_contig.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run_keep_unmapped.out.reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_none_for_prodigal.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_check_contigs_to_use.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_find_circular_using_prodigal.ctgs.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.expected.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_write_act_files.expected.crunch -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_init_ignore_ids -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph_or_contig_paths copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph_or_contig_paths/contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph_or_contig_paths copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_exclude_region.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run_keep_unmapped.out.reads.fq -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_index_fasta.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_write_act_files.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_max_length_from_fasta_file.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_region_start.reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_break_reads.broken_reads.fq -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_bit_of_everything.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_pair.test1.coords -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_load_nucmer_hits.coords -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_ignore_all.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/clean_test_write_log.log -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.reassembly.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assemble_test_rename_canu_contigs.in.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_hits_to_new_seq.1.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1 copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/contigs.paths -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1 copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1 copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/assembly_graph.fastg -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1 copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/minimus2_test_run_initial_merge.expected.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_pair.test3.coords -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_exclude_region.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.expected.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_write_act_files.qry.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_none_for_prodigal.expect.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_bit_of_everything.ignore -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_hits_to_new_seq.2.expected.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_hits_to_new_seq.2.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_rearrange_contigs.refs.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.expected.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_bit_of_everything.expect.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths/contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths/assembly_graph.fastg -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run.make_reads_and_bam.sh -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run_with_qual.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_ignore_all.expect.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/assembly_test_get_contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_run_no_qual.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_get_region_end.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/start_fixer_run_none_for_prodigal.ctg.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/data/bamfilter_test_break_reads.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/bamfilter_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/minimus2_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/common_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/external_progs_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/assembly_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/dnaa_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/mapping_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/assemble_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tests/clean_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/__pycache__/common.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/__pycache__/mapping.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/__pycache__/program.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/__pycache__/assembly.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/__pycache__/clean.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/__pycache__/bamfilter.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/__pycache__/merge.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/__pycache__/minimus2.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/__pycache__/assemble.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/__pycache__/versions.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/__pycache__/start_fixer.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/__pycache__/external_progs.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/__pycache__/dnaa.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/versions.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/data/dnaA.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/data/test_make_data.sh -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/data/test_for_reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/data/test_reads.fq.gz -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/data/test_ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/data/test_ref.fa.fai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/data/test_contigs.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/clean.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/bamfilter.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/all.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/version.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/progcheck.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/__pycache__/progcheck.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/__pycache__/clean.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/__pycache__/mapreads.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/__pycache__/merge.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/__pycache__/minimus2.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/__pycache__/all.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/__pycache__/assemble.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/__pycache__/version.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/__pycache__/bam2reads.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/__pycache__/fixstart.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/__pycache__/get_dnaa.cpython-312.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/clean.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/fixstart.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/assemble.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/mapreads.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/bam2reads.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/minimus2.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/__init__.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/merge.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/tasks/get_dnaa.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/assemble.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/minimus2.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/__init__.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/dnaa.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/merge.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/start_fixer.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.12/build/circlator/assembly.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/external_progs.py to external_progs.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/mapping.py to mapping.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/common.py to common.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/program.py to program.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/start_fixer_test.py to start_fixer_test.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/merge_test.py to merge_test.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/bamfilter_test.py to bamfilter_test.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/minimus2_test.py to minimus2_test.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/common_test.py to common_test.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/external_progs_test.py to external_progs_test.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/assembly_test.py to assembly_test.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/dnaa_test.py to dnaa_test.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/mapping_test.py to mapping_test.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/assemble_test.py to assemble_test.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tests/clean_test.py to clean_test.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/versions.py to versions.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/clean.py to clean.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/bamfilter.py to bamfilter.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/all.py to all.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/version.py to version.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/progcheck.py to progcheck.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/clean.py to clean.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/test.py to test.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/fixstart.py to fixstart.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/assemble.py to assemble.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/mapreads.py to mapreads.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/bam2reads.py to bam2reads.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/minimus2.py to minimus2.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/merge.py to merge.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/tasks/get_dnaa.py to get_dnaa.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/assemble.py to assemble.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/minimus2.py to minimus2.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/dnaa.py to dnaa.cpython-312.pyc /usr/lib/python3.12/dist-packages/circlator/dnaa.py:18: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/merge.py to merge.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/start_fixer.py to start_fixer.cpython-312.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator/assembly.py to assembly.cpython-312.pyc running install_egg_info running egg_info creating circlator.egg-info writing circlator.egg-info/PKG-INFO writing dependency_links to circlator.egg-info/dependency_links.txt writing requirements to circlator.egg-info/requires.txt writing top-level names to circlator.egg-info/top_level.txt writing manifest file 'circlator.egg-info/SOURCES.txt' reading manifest file 'circlator.egg-info/SOURCES.txt' adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'circlator.egg-info/SOURCES.txt' Copying circlator.egg-info to /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.12/dist-packages/circlator-1.5.5.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/bin copying build/scripts-3.12/circlator -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/bin changing mode of /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/bin/circlator to 755 I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/circlator-1.5.6/debian/circlator running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_scripts running install_lib creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11 creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/external_progs.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/mapping.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/common.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/program.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/start_fixer_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/merge_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/__pycache__/assemble_test.cpython-311-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/__pycache__/start_fixer_test.cpython-311-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/__pycache__/minimus2_test.cpython-311-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/__pycache__/mapping_test.cpython-311-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/__pycache__/external_progs_test.cpython-311-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/__pycache__/bamfilter_test.cpython-311-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/__pycache__/merge_test.cpython-311-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/__pycache__/common_test.cpython-311-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/__pycache__/dnaa_test.cpython-311-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/__pycache__/assembly_test.cpython-311-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/__pycache__/clean_test.cpython-311-pytest-8.1.2.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/__pycache__ creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_nucmer_hits_to_potential_join.reassembly.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_find_circular_using_promer.contigs.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test.dummy_input_assembly.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_nucmer_hits_to_potential_join.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_from_spades_after_3_6_1.assembly_graph.fastg -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_rearrange_contigs.in.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/mapping_test_aligned_read_to_read.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_write_act_files.expected.sh -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_from_canu.gfa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_init_dnaA.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_no_fastg copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_no_fastg/contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_no_fastg copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_rearrange_contigs.expect.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test_run_initial_merge.in.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_region_end.reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok/contigs.fastg -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok/contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_all_reads_from_contig.reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_exclude_region.reads.fq -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.reassembly.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run.reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_rearrange_contigs.expect.log -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_all_reads_from_contig.reads.fq -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.expected.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run.ref.fa.fai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/mapping_test_aligned_read_to_read.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assemble_test.dummy_reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_exclude_region.reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.reads.fq -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_only_contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_hits_to_new_seq.1.expected.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test_run_minimus2_on_each_contig.expected.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_bit_of_everything.ctg.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/mapping_test_bwa_mem.ref.fa.fai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_region_end.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_ref_lengths.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_init_contigs.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/clean_test_remove_small_contigs.out.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run_discard_unmapped.out.reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_ignore_all.to_ignore -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph/contigs.paths -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph/contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_original.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.in.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test_run_minimus2_on_each_contig.in.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.reassembly.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_pair.test2.coords -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/mapping_test_bwa_index.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_write_act_files.coords -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_find_circular_using_promer.refs.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_spades_contigs_paths_to_dict.contigs.paths -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_check_contigs_to_use.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_all_reads_from_contig.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assemble_test_rename_canu_contigs.expect.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/mapping_test_aligned_read_to_read.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/contigs.paths -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/assembly_graph.fastg -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/clean_test_contigs_to_keep -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.ignore.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/common_test_file_exists -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.reassembly.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.expected.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/clean_test_clean_contigs.in.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/mapping_test_bwa_mem.reads.fq -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_from_spades_after_3_6_1.contigs.paths -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run_no_qual.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_get_spades_circular_nodes.fastg -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_region_start.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1 copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1/contigs.fastg -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1 copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1/contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1 copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_all_reads_from_contig.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_index_fasta.fa.fai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_region_start.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_hits_to_new_seq.1.reassembly.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_contigs_dict_to_file.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run_with_qual.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_contigs_to_use.infile -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_break_reads.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_break_reads.broken_reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test_run_minimus2.in.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/clean_test_clean_contigs.out.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_write_renamed_contigs.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_from_spades_before_3_6_1.fastg -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/clean_test_load_nucmer_hits.coords -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_contigs_to_use.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.in.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/clean_test_remove_small_contigs.in.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/mapping_test_aligned_read_to_read.reads.fq -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_reassembly.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/mapping_test_bwa_mem.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_hits_to_new_seq.2.reassembly.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test.write_split_contig.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run_keep_unmapped.out.reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_none_for_prodigal.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_check_contigs_to_use.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_find_circular_using_prodigal.ctgs.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.expected.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_write_act_files.expected.crunch -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_init_ignore_ids -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph_or_contig_paths copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph_or_contig_paths/contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph_or_contig_paths copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_exclude_region.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run_keep_unmapped.out.reads.fq -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_index_fasta.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_write_act_files.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_max_length_from_fasta_file.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_region_start.reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_break_reads.broken_reads.fq -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_bit_of_everything.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_pair.test1.coords -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_load_nucmer_hits.coords -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_ignore_all.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/clean_test_write_log.log -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.reassembly.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assemble_test_rename_canu_contigs.in.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_hits_to_new_seq.1.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1 copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/contigs.paths -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1 copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1 copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/assembly_graph.fastg -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1 copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/minimus2_test_run_initial_merge.expected.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_pair.test3.coords -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_exclude_region.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.expected.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_write_act_files.qry.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_none_for_prodigal.expect.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_bit_of_everything.ignore -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_hits_to_new_seq.2.expected.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_hits_to_new_seq.2.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_rearrange_contigs.refs.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.expected.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_bit_of_everything.expect.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths/contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths/assembly_graph.fastg -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run.make_reads_and_bam.sh -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run_with_qual.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_ignore_all.expect.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/assembly_test_get_contigs.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_run_no_qual.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_get_region_end.bam.bai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/start_fixer_run_none_for_prodigal.ctg.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/data/bamfilter_test_break_reads.bam -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/bamfilter_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/minimus2_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/common_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/external_progs_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/assembly_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/dnaa_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/mapping_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/assemble_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tests/clean_test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/__pycache__/clean.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/__pycache__/dnaa.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/__pycache__/merge.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/__pycache__/mapping.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/__pycache__/program.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/__pycache__/assembly.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/__pycache__/external_progs.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/__pycache__/bamfilter.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/__pycache__/versions.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/__pycache__/assemble.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/__pycache__/start_fixer.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/__pycache__/common.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/__pycache__/minimus2.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/versions.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/data/dnaA.fasta -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/data/test_make_data.sh -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/data/test_for_reads.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/data/test_reads.fq.gz -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/data/test_ref.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/data/test_ref.fa.fai -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/data/test_contigs.fa -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/data copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/clean.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/bamfilter.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/all.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/version.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/progcheck.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks creating /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/__pycache__/clean.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/__pycache__/mapreads.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/__pycache__/merge.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/__pycache__/fixstart.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/__pycache__/version.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/__pycache__/progcheck.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/__pycache__/bam2reads.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/__pycache__/all.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/__pycache__/assemble.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/__pycache__/get_dnaa.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/__pycache__/minimus2.cpython-311.pyc -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/__pycache__ copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/clean.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/test.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/fixstart.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/assemble.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/mapreads.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/bam2reads.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/minimus2.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/__init__.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/merge.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/tasks/get_dnaa.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/assemble.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/minimus2.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/__init__.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/dnaa.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/merge.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/start_fixer.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator copying /build/reproducible-path/circlator-1.5.6/.pybuild/cpython3_3.11/build/circlator/assembly.py -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/external_progs.py to external_progs.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/mapping.py to mapping.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/common.py to common.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/program.py to program.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/start_fixer_test.py to start_fixer_test.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/merge_test.py to merge_test.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/bamfilter_test.py to bamfilter_test.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/minimus2_test.py to minimus2_test.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/common_test.py to common_test.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/external_progs_test.py to external_progs_test.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/assembly_test.py to assembly_test.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/dnaa_test.py to dnaa_test.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/mapping_test.py to mapping_test.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/assemble_test.py to assemble_test.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tests/clean_test.py to clean_test.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/versions.py to versions.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/clean.py to clean.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/bamfilter.py to bamfilter.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/all.py to all.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/version.py to version.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/progcheck.py to progcheck.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/clean.py to clean.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/test.py to test.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/fixstart.py to fixstart.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/assemble.py to assemble.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/mapreads.py to mapreads.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/bam2reads.py to bam2reads.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/minimus2.py to minimus2.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/merge.py to merge.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/tasks/get_dnaa.py to get_dnaa.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/assemble.py to assemble.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/minimus2.py to minimus2.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/dnaa.py to dnaa.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/merge.py to merge.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/start_fixer.py to start_fixer.cpython-311.pyc byte-compiling /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator/assembly.py to assembly.cpython-311.pyc running install_egg_info running egg_info writing circlator.egg-info/PKG-INFO writing dependency_links to circlator.egg-info/dependency_links.txt writing requirements to circlator.egg-info/requires.txt writing top-level names to circlator.egg-info/top_level.txt reading manifest file 'circlator.egg-info/SOURCES.txt' adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'circlator.egg-info/SOURCES.txt' Copying circlator.egg-info to /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/lib/python3.11/dist-packages/circlator-1.5.5.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.11/circlator -> /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/bin changing mode of /build/reproducible-path/circlator-1.5.6/debian/circlator/usr/bin/circlator to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/circlator-1.5.6' dh_installexamples cd debian/circlator/usr/share/doc/circlator/examples && tar caf data.tar.xz data --owner=0 --group=0 --numeric-owner --sort=name --mode=a+rX,og-w && rm -rf data make[1]: Leaving directory '/build/reproducible-path/circlator-1.5.6' dh_installman -O--buildsystem=pybuild 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_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'circlator' in '../circlator_1.5.6-11_all.deb'. dpkg-genbuildinfo --build=binary -O../circlator_1.5.6-11_amd64.buildinfo dpkg-genchanges --build=binary -O../circlator_1.5.6-11_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/1108397 and its subdirectories I: Current time: Sat Jun 28 12:49:19 -12 2025 I: pbuilder-time-stamp: 1751158159 Sun May 26 18:26:21 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Sun May 26 18:26:21 UTC 2024 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Sun May 26 18:28:56 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Sun May 26 18:28:57 UTC 2024 I: circlator_1.5.6-11_amd64.changes: Format: 1.8 Date: Sun, 03 Dec 2023 03:04:05 +0530 Source: circlator Binary: circlator Architecture: all Version: 1.5.6-11 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: circlator - circularize genome assemblies Closes: 1056234 Changes: circlator (1.5.6-11) unstable; urgency=medium . * Team Upload. * Do not run build-time tests by hand, rely on pybuild; copy test dir to {build_dir}/circlator before testing * Replace LooseVersion usage with packaging.version.parse (Closes: #1056234) Checksums-Sha1: cc0e428dcbd4c14bc684fef14ad3af1bc80e3652 4604712 circlator_1.5.6-11_all.deb 2bfc39ce67976b9f0b616c77bb5106faae3ce5f0 9557 circlator_1.5.6-11_amd64.buildinfo Checksums-Sha256: 4697b385e5a46b00c3390ff977c422998106bed0390bcc2b424f8d20cfe2c7f7 4604712 circlator_1.5.6-11_all.deb c97379e0129ef101dfa68ffedfab57f14bb8cc1b7e1192d54788cd8cfac7e9e1 9557 circlator_1.5.6-11_amd64.buildinfo Files: 09652a9f7dc049c2000998c297a8b055 4604712 science optional circlator_1.5.6-11_all.deb 34c2dd1300e792985b73774ba8ba4ec8 9557 science optional circlator_1.5.6-11_amd64.buildinfo Sun May 26 18:28:58 UTC 2024 I: diffoscope 268 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_4-21452.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.wQQTTAFS/circlator_1.5.6-11.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.wQQTTAFS/circlator_1.5.6-11.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.wQQTTAFS/circlator_1.5.6-11.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.wQQTTAFS/b1/circlator_1.5.6-11_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.wQQTTAFS/b2/circlator_1.5.6-11_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.451s) 0.451s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.063s) 0.063s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 856ms CPU time consumed: 857ms Sun May 26 19:01:49 UTC 2024 I: diffoscope 268 found no differences in the changes files, and a .buildinfo file also exists. Sun May 26 19:01:49 UTC 2024 I: circlator from unstable built successfully and reproducibly on amd64. Sun May 26 19:01:55 UTC 2024 I: Submitting .buildinfo files to external archives: Sun May 26 19:01:55 UTC 2024 I: Submitting 12K b1/circlator_1.5.6-11_amd64.buildinfo.asc Sun May 26 19:02:17 UTC 2024 I: Submitting 12K b2/circlator_1.5.6-11_amd64.buildinfo.asc Sun May 26 19:02:44 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun May 26 19:02:44 UTC 2024 I: Done submitting .buildinfo files. Sun May 26 19:02:44 UTC 2024 I: Removing signed circlator_1.5.6-11_amd64.buildinfo.asc files: removed './b1/circlator_1.5.6-11_amd64.buildinfo.asc' removed './b2/circlator_1.5.6-11_amd64.buildinfo.asc'