I: pbuilder: network access will be disabled during build I: Current time: Thu Apr 2 03:12:33 -12 2026 I: pbuilder-time-stamp: 1775142753 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 [ariba_2.14.7+ds-7.dsc] I: copying [./ariba_2.14.7+ds.orig.tar.xz] I: copying [./ariba_2.14.7+ds-7.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./ariba_2.14.7+ds-7.dsc: unsupported subcommand dpkg-source: info: extracting ariba in ariba-2.14.7+ds dpkg-source: info: unpacking ariba_2.14.7+ds.orig.tar.xz dpkg-source: info: unpacking ariba_2.14.7+ds-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs_for_extension.patch dpkg-source: info: applying use_bwa_compatible_fermi-lite.patch dpkg-source: info: applying add-testdata.patch dpkg-source: info: applying disable-tests-with-internet-access.patch dpkg-source: info: applying support-pymummer-0.11.patch dpkg-source: info: applying run-debian-spades-wrapper.patch dpkg-source: info: applying python3.12.patch dpkg-source: info: applying python3.12_syntax_warning.patch dpkg-source: info: applying py3.13.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/861276/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='cfb90d5e7d834346a31d2033108e8ea0' 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='861276' 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.MyhnfygG/pbuilderrc_38Sm --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.MyhnfygG/b1 --logfile b1/build.log ariba_2.14.7+ds-7.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 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/861276/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-biopython, python3-all-dev, python3-dendropy, python3-setuptools, python3-pymummer, python3-pysam, python3-pytest, python3-bs4, python3-matplotlib, python3-tk, bowtie2, cd-hit, mash, libminimap-dev, libfml-dev, mummer, fastaq, help2man, asciidoctor, spades dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19779 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-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-dendropy; however: Package python3-dendropy is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pymummer; however: Package python3-pymummer is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-bs4; however: Package python3-bs4 is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-tk; however: Package python3-tk is not installed. pbuilder-satisfydepends-dummy depends on bowtie2; however: Package bowtie2 is not installed. pbuilder-satisfydepends-dummy depends on cd-hit; however: Package cd-hit is not installed. pbuilder-satisfydepends-dummy depends on mash; however: Package mash is not installed. pbuilder-satisfydepends-dummy depends on libminimap-dev; however: Package libminimap-dev is not installed. pbuilder-satisfydepends-dummy depends on libfml-dev; however: Package libfml-dev is not installed. pbuilder-satisfydepends-dummy depends on mummer; however: Package mummer is not installed. pbuilder-satisfydepends-dummy depends on fastaq; however: Package fastaq is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor is not installed. pbuilder-satisfydepends-dummy depends on spades; however: Package spades is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bamtools{a} blt{a} bowtie2{a} bsdextrautils{a} bwa{a} ca-certificates{a} cd-hit{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fastaq{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lyx{a} fonts-urw-base35{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbamtools2.5.2{a} libblas3{a} libbrotli1{a} libcairo2{a} libcapnp-1.1.0{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfml-dev{a} libfml0{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgcrypt20{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgpg-error0{a} libgraphite2-3{a} libgsl28{a} libgslcblas0{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-0{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap2{a} liblerc4{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libminimap-dev{a} libminimap0{a} libmurmurhash2{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnlopt0{a} libopenjp2-7{a} libp11-kit0{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libruby{a} libruby3.3{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsigsegv2{a} libspoa7.0.0{a} libssh2-1t64{a} libssw0{a} libtasn1-6{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} m4{a} man-db{a} mash{a} media-types{a} mummer{a} netbase{a} openssl{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-all-dev{a} python3-attr{a} python3-autocommand{a} python3-biopython{a} python3-brotli{a} python3-bs4{a} python3-cairo{a} python3-chardet{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dendropy{a} python3-dev{a} python3-fonttools{a} python3-freetype{a} python3-fs{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-joblib{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-pymummer{a} python3-pyparsing{a} python3-pysam{a} python3-pytest{a} python3-pytz{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-soupsieve{a} python3-sympy{a} python3-tk{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-yaml{a} python3-zipp{a} python3.12-tk{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} rake{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-did-you-mean{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rubygems{a} ruby-test-unit{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.3{a} rubygems-integration{a} samtools{a} sensible-utils{a} sgml-base{a} spades{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-dejavu-extra fonts-lato isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libgpg-error-l10n libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-cssselect python3-html5lib python3-olefile python3-pooch python3-psutil python3-pygments ruby-sdbm shared-mime-info wget xdg-user-dirs zip 0 packages upgraded, 245 newly installed, 0 to remove and 0 not upgraded. Need to get 173 MB of archives. After unpacking 670 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libsigsegv2 amd64 2.14-1+b2 [34.4 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 gawk amd64 1:5.2.1-2+b1 [674 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.2-1 [27.1 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 media-types all 12.0.0 [28.9 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.2-1 [10.0 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.2-1 [28.1 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-2+b1 [138 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.3+ds-2+b1 [5081 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.4.1-1 [1427 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.19 [5488 B] Get: 39 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 ruby-did-you-mean all 1.6.3-2 [20.9 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 ruby-minitest all 5.25.4-2 [66.2 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 ruby-power-assert all 2.0.3-1 [11.8 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 ruby-test-unit all 3.6.2-1 [79.1 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libruby3.3 amd64 3.3.7-1 [6274 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 ruby3.3 amd64 3.3.7-1 [827 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.3+b1 [5440 B] Get: 51 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.6.3-1 [406 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.3+b1 [6560 B] Get: 53 http://deb.debian.org/debian unstable/main amd64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 asciidoctor all 2.0.23-1 [88.7 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6+b1 [161 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 bamtools amd64 2.5.2+dfsg-6+b1 [207 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.47-1 [282 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 74 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get: 88 http://deb.debian.org/debian unstable/main amd64 bowtie2 amd64 2.5.4-1+b1 [1508 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 bwa amd64 0.7.18-1 [212 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 cd-hit amd64 4.8.1-4 [522 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 97 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 112 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.8.0-1 [222 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.8.0-1 [724 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250108 [113 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 126 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.12.1-3 [365 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5+20250216-1 [105 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.21-1 [667 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 fastaq all 3.17.0-9 [47.8 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.3-1 [190 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libcapnp-1.1.0 amd64 1.1.0-2 [1479 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libfml0 amd64 0.1+git20221215.85f159e-1 [70.1 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libfml-dev amd64 0.1+git20221215.85f159e-1 [82.0 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.83.4-1 [1512 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libminimap0 amd64 0.2-8+b3 [22.7 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libminimap-dev amd64 0.2-8+b3 [33.5 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libmurmurhash2 amd64 1.6-1+b1 [6180 B] Get: 177 http://deb.debian.org/debian unstable/main amd64 libnlopt0 amd64 2.7.1-6+b4 [178 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-1 [204 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.2-1 [2151 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.2-1 [5005 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.2-1 [10.3 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.13.2-1 [1068 B] Get: 183 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libspoa7.0.0 amd64 4.1.4-2+b1 [74.1 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-15+b2 [21.8 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 mash amd64 2.3+dfsg-6+b2 [192 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 mummer amd64 3.23+dfsg-8 [662 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.8.3-7 [2735 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.2-1 [1048 B] Get: 197 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.2-1 [507 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.2-1 [26.1 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.13.2-1 [1068 B] Get: 200 http://deb.debian.org/debian unstable/main amd64 python3-attr all 25.1.0-1 [68.7 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 python3.12-tk amd64 3.12.9-1 [113 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 python3.13-tk amd64 3.13.2-1 [103 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.13.1-1+b1 [9760 B] Get: 205 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 11.1.0-5+b1 [81.6 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 11.1.0-5+b1 [513 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 python3-cairo amd64 1.26.1-2+b2 [114 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 210 http://deb.debian.org/debian unstable/main amd64 python3-reportlab all 4.3.1-1 [1158 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 python3-biopython amd64 1.85+dfsg-2+b1 [1672 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b7 [320 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 python3-soupsieve all 2.6-1 [38.3 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 python3-bs4 all 4.13.3-1 [166 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.3.1-1+b1 [216 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get: 219 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 python3-dendropy all 4.6.1-2 [277 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 python3-pytz all 2025.1-3 [150 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 python3-tz all 2025.1-3 [4004 B] Get: 224 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-6 [95.1 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 5.3.1-1+b1 [1288 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.4.0+dfsg-1+b1 [25.5 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.14.1-4+b1 [17.1 MB] Get: 229 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.13.3-5 [4148 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.55.3-2+b1 [1448 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 235 http://deb.debian.org/debian unstable/main amd64 python3-joblib all 1.4.2-3 [216 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.7-3+b1 [62.0 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.8.3-7+b1 [23.0 MB] Get: 240 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 python3-pymummer all 0.11.0-5 [18.1 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 python3-pysam amd64 0.23.0+ds-1+b1 [3665 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.3.4-1 [250 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-1+b2 [136 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 spades amd64 4.0.0+dfsg1-2 [8071 kB] Fetched 173 MB in 5s (36.3 MB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19779 files and directories currently installed.) Preparing to unpack .../readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../libreadline8t64_8.2-6_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 (8.2-6) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../libsigsegv2_2.14-1+b2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.14-1+b2) ... Setting up readline-common (8.2-6) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up libsigsegv2:amd64 (2.14-1+b2) ... Selecting previously unselected package gawk. (Reading database ... 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Setting up libmurmurhash2:amd64 (1.6-1+b1) ... Setting up ruby-power-assert (2.0.3-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up gawk (1:5.2.1-2+b1) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-2) ... Setting up bwa (0.7.18-1) ... Setting up fonts-lyx (2.4.3-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.23-1+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libgcrypt20:amd64 (1.11.0-7) ... Setting up libqhull-r8.0:amd64 (2020.2-6+b2) ... Setting up libnlopt0:amd64 (2.7.1-6+b4) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libcom-err2:amd64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libfml0:amd64 (0.1+git20221215.85f159e-1) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-4) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8+b1) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Apr 2 15:13:31 UTC 2026. Universal Time is now: Thu Apr 2 15:13:31 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... Setting up ruby-minitest (5.25.4-2) ... Setting up libminimap0:amd64 (0.2-8+b3) ... Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libexpat1-dev:amd64 (2.6.4-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3.1) ... Setting up ruby-test-unit (3.6.2-1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libjsoncpp26:amd64 (1.9.6-3) ... Setting up libncurses6:amd64 (6.5+20250216-1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up libproc2-0:amd64 (2:4.0.4-7) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libspoa7.0.0:amd64 (4.1.4-2+b1) ... Setting up libpng16-16t64:amd64 (1.6.47-1) ... Setting up python3-numpy-dev:amd64 (1:2.2.3+ds-2+b1) ... Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... 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Setting up libngtcp2-16:amd64 (1.9.1-1) ... Setting up sgml-base (1.31) ... Setting up libcapnp-1.1.0:amd64 (1.1.0-2) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up ruby-did-you-mean (1.6.3-2) ... Setting up libgsl28:amd64 (2.8+dfsg-5) ... Setting up python-matplotlib-data (3.8.3-7) ... Setting up openssl (3.4.1-1) ... Setting up libwebpmux3:amd64 (1.5.0-0.1) ... Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ... Setting up libssw0:amd64 (1.1-15+b2) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Setting up libldap2:amd64 (2.6.9+dfsg-1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libpython3-stdlib:amd64 (3.13.2-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpython3.13:amd64 (3.13.2-1) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libfml-dev:amd64 (0.1+git20221215.85f159e-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b4) ... Setting up libtool (2.5.4-3) ... Setting up python3.13 (3.13.2-1) ... Setting up fontconfig-config (2.15.0-2) ... Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up python3 (3.13.2-1) ... Setting up libidn2-0:amd64 (2.3.7-2+b1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-platformdirs (4.3.6-1) ... Setting up bowtie2 (2.5.4-1+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up python3-decorator (5.1.1-5) ... Setting up libglib2.0-0t64:amd64 (2.83.4-1) ... No schema files found: doing nothing. Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up python3-brotli (1.1.0-2+b7) ... Setting up libpython3.13-dev:amd64 (3.13.2-1) ... Setting up python3-cycler (0.12.1-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up python3-kiwisolver (1.4.7-3+b1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up mash (2.3+dfsg-6+b2) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-numpy (1:2.2.3+ds-2+b1) ... Setting up libminimap-dev:amd64 (0.2-8+b3) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up python3-pluggy (1.5.0-1) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1.1+b1) ... Setting up libharfbuzz0b:amd64 (10.2.0-1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-contourpy (1.3.1-1+b1) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-dendropy (4.6.1-2) ... Setting up python3-soupsieve (2.6-1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.13.3-5) ... Setting up python3-attr (25.1.0-1) ... Setting up libxft2:amd64 (2.3.6-1+b4) ... Setting up python3-scipy (1.14.1-4+b1) ... Setting up libpython3-dev:amd64 (3.13.2-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-joblib (1.4.2-3) ... Setting up python3-lz4 (4.4.0+dfsg-1+b1) ... Setting up python3.13-dev (3.13.2-1) ... Setting up python3-pytest (8.3.4-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.16-1) ... Setting up python3-typeguard (4.4.2-1) ... Setting up python3.12-tk (3.12.9-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3-all (3.13.2-1) ... Setting up python3-yaml (6.0.2-1+b2) ... Setting up python3-pytz (2025.1-3) ... Setting up rubygems-integration (1.19) ... Setting up python3-freetype (2.5.1-1) ... Setting up xfonts-utils (1:7.7+7) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.2-2) ... Setting up python3.13-tk (3.13.2-1) ... Setting up python3-tz (2025.1-3) ... Setting up python3-bs4 (4.13.3-1) ... Setting up python3-fs (2.4.16-6) ... Setting up python3-inflect (7.3.1-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libpython3-all-dev:amd64 (3.13.2-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up libraqm0:amd64 (0.10.2-1) ... Setting up python3-dev (3.13.2-1) ... Setting up python3-lxml:amd64 (5.3.1-1+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up python3-pkg-resources (75.8.0-1) ... Setting up python3-all-dev (3.13.2-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up python3-cairo (1.26.1-2+b2) ... Setting up python3-setuptools (75.8.0-1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up libcurl3t64-gnutls:amd64 (8.12.1-3) ... Setting up python3-tk:amd64 (3.13.1-1+b1) ... Setting up debhelper (13.24.1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-pil:amd64 (11.1.0-5+b1) ... Setting up python3-pil.imagetk:amd64 (11.1.0-5+b1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-reportlab (4.3.1-1) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up dh-python (6.20250108) ... Setting up python3-pysam (0.23.0+ds-1+b1) ... Setting up samtools (1.21-1) ... Setting up spades (4.0.0+dfsg1-2) ... Setting up fastaq (3.17.0-9) ... Setting up python3-pymummer (0.11.0-5) ... Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... Setting up libruby3.3:amd64 (3.3.7-1) ... Setting up ruby-rubygems (3.6.3-1) ... Setting up python3-fonttools (4.55.3-2+b1) ... Setting up ruby3.3 (3.3.7-1) ... Setting up python3-matplotlib (3.8.3-7+b1) ... Setting up libruby:amd64 (1:3.3+b1) ... Setting up ruby (1:3.3+b1) ... Setting up ruby-asciidoctor (2.0.23-1) ... Setting up rake (13.2.1-1) ... Setting up asciidoctor (2.0.23-1) ... Processing triggers for libc-bin (2.40-7) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.85+dfsg-2+b1) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/ariba-2.14.7+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../ariba_2.14.7+ds-7_source.changes dpkg-buildpackage: info: source package ariba dpkg-buildpackage: info: source version 2.14.7+ds-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/ariba-2.14.7+ds' rm -rf /build/reproducible-path/ariba-2.14.7+ds/debian/man dh_auto_clean -- I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running clean removing '/build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it make[1]: Leaving directory '/build/reproducible-path/ariba-2.14.7+ds' 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: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running build running build_py creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/external_progs.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/megares_zip_parser.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/flag.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/mapping.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/mlst_profile.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/common.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/versions.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/reference_data.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/summary_cluster.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/clusters.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/assembly_compare.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/link.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/refdata_query.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/mlst_reporter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/report_filter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/summary.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/report_flag_expander.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/aln_to_metadata.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/samtools_variants.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/summary_sample.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/cdhit.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/megares_data_finder.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/cluster.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/ref_genes_getter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/bam_parse.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/mic_plotter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/vfdb_parser.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/read_store.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/sequence_variant.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/assembly_variants.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/pubmlst_ref_preparer.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/faidx.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/pubmlst_getter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/report.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/scaffold_graph.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/read_filter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/histogram.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/tb.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/ref_seq_chooser.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/summary_cluster_variant.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/card_record.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/sequence_metadata.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/assembly.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba copying ariba/ref_preparer.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/ref_genes_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/histogram_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/test_refdata_query.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/summary_sample_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/read_store_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/link_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/mic_plotter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/reference_data_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/scaffold_graph_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/summary_cluster_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/aln_to_metadata_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/megares_zip_parser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/bam_parse_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/flag_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/megares_data_finder_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/pubmlst_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/samtools_variants_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/clusters_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/vfdb_parser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/cluster_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/assembly_compare_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/versions_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/ref_preparer_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/cdhit_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/tb_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/common_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/external_progs_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/assembly_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/faidx_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/summary_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/read_filter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/pubmlst_ref_preparer_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/sequence_metadata_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/mapping_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/mlst_profile_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/sequence_variant_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/ncbi_getter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/assembly_variants_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/summary_cluster_variant_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/ref_seq_chooser_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/report_flag_expander_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/mlst_reporter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/card_record_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests copying ariba/tests/report_filter_test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks copying ariba/tasks/flag.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks copying ariba/tasks/version.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks copying ariba/tasks/prepareref_tb.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks copying ariba/tasks/getref.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks copying ariba/tasks/refquery.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks copying ariba/tasks/aln2meta.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks copying ariba/tasks/test.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks copying ariba/tasks/pubmlstspecies.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks copying ariba/tasks/summary.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks copying ariba/tasks/run.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks copying ariba/tasks/__init__.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks copying ariba/tasks/expandflag.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks copying ariba/tasks/reportfilter.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks copying ariba/tasks/prepareref.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks copying ariba/tasks/micplot.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks copying ariba/tasks/pubmlstget.py -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tasks creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data copying ariba/test_run_data/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data copying ariba/test_run_data/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data copying ariba/test_run_data/metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data copying ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data copying ariba/test_run_data/ref_seqs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/test_run_data creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20190102.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181221.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20190102.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181221.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181115.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data copying ariba/tb_data/NC_000962.3.gb -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data copying ariba/tb_data/NC_000962.3.fa.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181115.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tb_data creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_fasta_file.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_check_spades_log_file.log.bad -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_count_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.3.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.4.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_whole_run.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_too_long.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variants.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_cat_genes_match_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/vfdb_parser_test_run.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_init_refdata.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_rename_sequences.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_rename_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_init_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_whole_run.out.csv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_count_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_fails.empty.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.rename.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/refdata_query_prepareref.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_rename_seqs.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.profile.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_load_file.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_db.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_fails.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/summary_to_matrix.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/vfdb_parser_test_run.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.out.cluster -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_load_annotations.csv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_sort_file.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_profile_test.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_rename_sequences.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.params.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_load_fofn -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parse_extract_files_ok.zip -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_run.expected.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence_type.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.1.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.in.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_init_bad.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_db.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_remove_bad_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/report_flag_expander.run.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_var_groups.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.in.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.read_store -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_profile_test.init.profile.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_metadata_tsvs.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_write_all_links_to_file.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_getter.dbases.xml -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_too_short.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/refdata_query_prepareref.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_write_distance_matrix.distances -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.smi -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_load_report_bad.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite.expected.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_init_refdata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_insert_codon.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/tb_report_to_resistance_dict.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_load_summary_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_not_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_clean.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.rename -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_load_input_files.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.ariba.report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_write_report.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_sort_file.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_whole_run.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_init.fofn -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_sam_to_fastq.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_fails.empty.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.in.3 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/report_flag_expander.run.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/tb_genbank_to_gene_coords.gb -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_load_input_files.1.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.ref.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_data_info_file -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_load_mic_file.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_unsorted.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_run.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_fasta_files.in.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/vfdb_parser_test_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/summary_to_matrix.2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_ok.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/dummy.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_load_report_good.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence_type.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.2.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.out -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.removed.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_fake_run.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_compress_and_index_file.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/00.rename_info -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/refdata_query_prepareref creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding copying ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding copying ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding copying ariba/tests/data/cluster_test_full_run_ok_non_coding/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run.out creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.rename_info -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/00.params.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_run_with_tb.ref creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail copying ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly copying ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene2.tfa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/profile.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files copying ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files copying ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files copying ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/megares_zip_parser_write_files creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2 copying ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2 copying ariba/tests/data/cluster_test_init_no_reads_2/genes.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only copying ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only copying ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only copying ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1 copying ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1 copying ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1 creating /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa -> /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene running build_ext building 'minimap_ariba' extension creating build/temp.linux-x86_64-cpython-313/ariba/ext x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ariba-2.14.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/minimap -I/usr/include/python3.13 -c ariba/ext/minimap_ariba.cpp -o build/temp.linux-x86_64-cpython-313/ariba/ext/minimap_ariba.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ariba-2.14.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/ariba-2.14.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/ariba/ext/minimap_ariba.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/minimap_ariba.cpython-313-x86_64-linux-gnu.so -lz -lminimap building 'fermilite_ariba' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ariba-2.14.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c ariba/ext/fml-asm_ariba.cpp -o build/temp.linux-x86_64-cpython-313/ariba/ext/fml-asm_ariba.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ariba-2.14.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/ariba-2.14.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/ariba/ext/fml-asm_ariba.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/fermilite_ariba.cpython-313-x86_64-linux-gnu.so -lz -lfml building 'vcfcall_ariba' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ariba-2.14.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -c ariba/ext/vcfcall_ariba.cpp -o build/temp.linux-x86_64-cpython-313/ariba/ext/vcfcall_ariba.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ariba-2.14.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/ariba-2.14.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/ariba/ext/vcfcall_ariba.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/vcfcall_ariba.cpython-313-x86_64-linux-gnu.so running build_scripts creating build/scripts-3.13 copying and adjusting scripts/ariba -> build/scripts-3.13 changing mode of build/scripts-3.13/ariba from 644 to 755 dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build; python3.13 -m pytest ============================= test session starts ============================== platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 rootdir: /build/reproducible-path/ariba-2.14.7+ds plugins: typeguard-4.4.2 collected 356 items ariba/tests/aln_to_metadata_test.py .................... [ 5%] ariba/tests/assembly_compare_test.py ................ [ 10%] ariba/tests/assembly_test.py ..F...... [ 12%] ariba/tests/assembly_variants_test.py ........... [ 15%] ariba/tests/bam_parse_test.py ...... [ 17%] ariba/tests/card_record_test.py ........ [ 19%] ariba/tests/cdhit_test.py ................ [ 24%] ariba/tests/cluster_test.py ............................. [ 32%] ariba/tests/clusters_test.py ................ [ 36%] ariba/tests/common_test.py .. [ 37%] ariba/tests/external_progs_test.py . [ 37%] ariba/tests/faidx_test.py . [ 37%] ariba/tests/flag_test.py ....... [ 39%] ariba/tests/histogram_test.py .... [ 41%] ariba/tests/link_test.py ......... [ 43%] ariba/tests/mapping_test.py ....... [ 45%] ariba/tests/megares_data_finder_test.py .. [ 46%] ariba/tests/megares_zip_parser_test.py ..... [ 47%] ariba/tests/mic_plotter_test.py ............. [ 51%] ariba/tests/mlst_profile_test.py .... [ 52%] ariba/tests/mlst_reporter_test.py ..... [ 53%] ariba/tests/pubmlst_getter_test.py ... [ 54%] ariba/tests/pubmlst_ref_preparer_test.py .. [ 55%] ariba/tests/read_filter_test.py . [ 55%] ariba/tests/read_store_test.py ....... [ 57%] ariba/tests/ref_genes_getter_test.py . [ 57%] ariba/tests/ref_preparer_test.py ..... [ 58%] ariba/tests/ref_seq_chooser_test.py ....... [ 60%] ariba/tests/reference_data_test.py .............................. [ 69%] ariba/tests/report_filter_test.py ................. [ 74%] ariba/tests/report_flag_expander_test.py . [ 74%] ariba/tests/samtools_variants_test.py ....... [ 76%] ariba/tests/scaffold_graph_test.py ..... [ 77%] ariba/tests/sequence_metadata_test.py ..... [ 79%] ariba/tests/sequence_variant_test.py ....... [ 81%] ariba/tests/summary_cluster_test.py ....................... [ 87%] ariba/tests/summary_cluster_variant_test.py .... [ 88%] ariba/tests/summary_sample_test.py .... [ 89%] ariba/tests/summary_test.py .................... [ 95%] ariba/tests/tb_test.py ....... [ 97%] ariba/tests/test_refdata_query.py ..... [ 98%] ariba/tests/versions_test.py . [ 99%] ariba/tests/vfdb_parser_test.py ... [100%] =================================== FAILURES =================================== ____________________ TestAssembly.test_assemble_with_spades ____________________ self = @unittest.skipUnless(extern_progs.exe('spades'), "Spades assembler is optional and is not configured") def test_assemble_with_spades(self): '''test _assemble_with_spades''' reads1 = os.path.join(data_dir, 'assembly_test_assemble_with_spades_reads_1.fq') reads2 = os.path.join(data_dir, 'assembly_test_assemble_with_spades_reads_2.fq') tmp_dir = 'tmp.test_assemble_with_spades' tmp_log = 'tmp.test_assemble_with_spades.log' with open(tmp_log, 'w') as tmp_log_fh: print('First line', file=tmp_log_fh) common.rmtree(tmp_dir) #using spades_options=" --only-assembler" because error correction cannot determine quality offset on this #artificial dataset a = assembly.Assembly(reads1, reads2, 'not needed', 'not needed', tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', tmp_log_fh, 'not needed', assembler="spades", spades_options=" --only-assembler") a._assemble_with_spades() > self.assertTrue(a.assembled_ok) E AssertionError: False is not true ariba/tests/assembly_test.py:128: AssertionError ----------------------------- Captured stderr call ----------------------------- WARNING: I tried to get the version of spades with: "/usr/bin/spades.py --version" and the output didn't match this regular expression: "SPAdes.*v([0-9\.]+)" The following command failed with exit code 4 ['/usr/bin/spades.py', '-t', '1', '--pe1-1', '/build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq', '--pe1-2', '/build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq', '-o', '/build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/tmp.test_assemble_with_spades/Assemble', '--only-assembler'] The output was: == Warning == No assembly mode was specified! If you intend to assemble high-coverage multi-cell/isolate data, use '--isolate' option. Command line: /usr/libexec/spades/spades.py -t 1 --pe1-1 /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq --pe1-2 /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -o /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/tmp.test_assemble_with_spades/Assemble --only-assembler System information: SPAdes version: 4.0.0 Python version: 3.13.2 OS: Linux-6.12.9+bpo-amd64-x86_64-with-glibc2.40 Output dir: /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/tmp.test_assemble_with_spades/Assemble Mode: ONLY assembling (without read error correction) Debug mode is turned OFF Dataset parameters: Standard mode For multi-cell/isolate data we recommend to use '--isolate' option; for single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq use '--rna'. Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq'] right reads: ['/build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq'] interlaced reads: not specified single reads: not specified merged reads: not specified Assembly parameters: k: automatic selection based on read length Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Assembly graph output will use GFA v1.2 format Other parameters: Dir for temp files: /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/tmp.test_assemble_with_spades/Assemble/tmp Threads: 1 Memory limit (in Gb): 78 ======= SPAdes pipeline started. Log can be found here: /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/tmp.test_assemble_with_spades/Assemble/spades.log /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq: max reads length: 76 /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq: max reads length: 76 Reads length: 76 ===== Before start started. ===== Assembling started. ===== K21 started. == Running: /usr/libexec/spades/spades-core /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/tmp.test_assemble_with_spades/Assemble/K21/configs/config.info Exception caught /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/tmp.test_assemble_with_spades/Assemble/K21/configs/config.info(3): cannot open include file simplification.info == Error == system call for: "['/usr/libexec/spades/spades-core', '/build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/tmp.test_assemble_with_spades/Assemble/K21/configs/config.info']" finished abnormally, OS return value: 4 None In case you have troubles running SPAdes, you can report an issue on our GitHub repository github.com/ablab/spades Please provide us with params.txt and spades.log files from the output directory. SPAdes log can be found here: /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/tmp.test_assemble_with_spades/Assemble/spades.log Thank you for using SPAdes! If you use it in your research, please cite: Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A. and Korobeynikov, A., 2020. Using SPAdes de novo assembler. Current protocols in bioinformatics, 70(1), p.e102. doi.org/10.1002/cpbi.102 =============================== warnings summary =============================== ariba/__init__.py:1 /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/__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 ../../../../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3 /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'locate_file', 'read_text'} __version__ = Distribution().from_name('pyfastaq').version .pybuild/cpython3_3.13_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours .pybuild/cpython3_3.13_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours .pybuild/cpython3_3.13_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/mic_plotter.py:222: MatplotlibDeprecationWarning: The get_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap(obj)`` instead. cmap = cmx.get_cmap(colormap) .pybuild/cpython3_3.13_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build/ariba/mic_plotter.py:206: MatplotlibDeprecationWarning: The get_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap(obj)`` instead. cmap = cmx.get_cmap(colormap) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED ariba/tests/assembly_test.py::TestAssembly::test_assemble_with_spades ============= 1 failed, 355 passed, 6 warnings in 82.05s (0:01:22) ============= E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/ariba-2.14.7+ds/.pybuild/cpython3_3.13_ariba/build; python3.13 -m pytest dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13 make: *** [debian/rules:16: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/861276 and its subdirectories