Running as unit: rb-build-arm64_15-71419.service ==================================================================================== Thu Nov 21 17:46:43 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_15) on jenkins, called using "codethink01-arm64 codethink04-arm64" as arguments. Thu Nov 21 17:46:43 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-fhmzQyGh" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Nov 21 17:46:43 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Thu Nov 21 17:46:43 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-ITxchS' Thu Nov 21 17:46:44 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Thu Nov 21 17:46:44 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-ZskQtz' ok, let's check if presto is building anywhere yet… ok, presto is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of presto in unstable on arm64 on jenkins now. 1st build will be done on codethink01-arm64.debian.net. 2nd build will be done on codethink04-arm64.debian.net. ============================================================================= Thu Nov 21 17:46:58 UTC 2024 I: starting to build presto/unstable/arm64 on jenkins on '2024-11-21 17:46' Thu Nov 21 17:46:58 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_15/71419/console.log 1732211218 arm64 unstable presto Thu Nov 21 17:46:58 UTC 2024 I: Downloading source for unstable/presto=0.7.2-1 --2024-11-21 17:46:58-- http://deb.debian.org/debian/pool/main/p/presto/presto_0.7.2-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2233 (2.2K) [text/prs.lines.tag] Saving to: ‘presto_0.7.2-1.dsc’ 0K .. 100% 348M=0s 2024-11-21 17:46:58 (348 MB/s) - ‘presto_0.7.2-1.dsc’ saved [2233/2233] --2024-11-21 17:46:58-- http://deb.debian.org/debian/pool/main/p/presto/presto_0.7.2-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2233 (2.2K) [text/prs.lines.tag] Saving to: ‘presto_0.7.2-1.dsc’ 0K .. 100% 348M=0s 2024-11-21 17:46:58 (348 MB/s) - ‘presto_0.7.2-1.dsc’ saved [2233/2233] Thu Nov 21 17:46:58 UTC 2024 I: presto_0.7.2-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: presto Binary: python3-presto, presto Architecture: any all Version: 0.7.2-1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Homepage: https://presto.readthedocs.io Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/presto Vcs-Git: https://salsa.debian.org/med-team/presto.git Testsuite: autopkgtest-pkg-pybuild Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all, python3-setuptools, python3-biopython , python3-pandas , python3-scipy , python3-packaging , vsearch [amd64 arm64 kfreebsd-amd64 ppc64el] , cd-hit Package-List: presto deb python optional arch=all python3-presto deb python optional arch=any Checksums-Sha1: 8e13875cb853e6bb06f77469942f36d565277791 361536 presto_0.7.2.orig.tar.xz 3066f884934bb7424d348c51c3b1cc356a47479d 20772 presto_0.7.2-1.debian.tar.xz Checksums-Sha256: 2eb8874e93df323a6fdf8a6e198f7795d710493d6a94d25d650a8ce0aa22c37b 361536 presto_0.7.2.orig.tar.xz 448a6926319a56a21569fc927e45b1708549ef27b7542ebfa345e0d8aab698d2 20772 presto_0.7.2-1.debian.tar.xz Files: c10efa18782dda0f00d1a99becd31881 361536 presto_0.7.2.orig.tar.xz 50274e92ddd35153efbe95fe0cb01b0b 20772 presto_0.7.2-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEESjHbWh7kCWyHOZiAkDZJKUwz+bcFAmXTTsYACgkQkDZJKUwz +bfRyA/9EBLWJf1DlmgkxNIsmCceB64EJXnGBG+Z14PKTA0sOlp53TW7dSlnGZcb yDWyBcbvj6IAlXBcG/XE0yVeuM17NXLXo9Y0jCe6EXYIxqiBs05hyj1xj5Z33831 +4niNjHXr9HsrvQx5ajNM0hpdqS8KRvpZiB5Xnzt2kOC61mBBkhe1gDCFvanOxnG wl2oA0oe23Ybje/zdu2Z5ob2rF2QwC+F48XuMzeLh2MixTkczvmq9pBuyk/dYvO2 N7c8nhaOnCQqeCkxdt1T/GpxeytiK7B0VEJK2NjXyThOlh4c4GMS7K5neeN9Y5Ic tqTVlzGgRsXWIqA4p/iALniS4kb0Zitx23csVf+IQdtT8MpOejia7d8ZjJ+kWX/B N2f0wZFbPqbTbkAJW7zklHO1Q6A0x9aMZKxxaHm5ptOcAw+ukf8pfr65yy/RfX4+ UIdBD06OGSCxGSFyV5ZBL8gSdTxoVsnwgKKrdhYdrwpEB+7AY7HqgC18nUAIOaql auDb2SU3d7Aon1dcCD+I/XWjlNb6W4gT7nWn5WM3RDLWhADcWRA62k5tx5L9XLOq CxfOgQpez26RtcikZksRDmoGfB0ekGCUwQvvTNSk69bpNqQaGz3fyEFSDuO8FRds xdrc3f/TWvY9axPIYtIjQJ95a3E05Q+XiGpT4pQjfl+dGSu5Pvc= =9L84 -----END PGP SIGNATURE----- Thu Nov 21 17:46:58 UTC 2024 I: Checking whether the package is not for us Thu Nov 21 17:46:58 UTC 2024 I: Starting 1st build on remote node codethink01-arm64.debian.net. Thu Nov 21 17:46:58 UTC 2024 I: Preparing to do remote build '1' on codethink01-arm64.debian.net. Thu Nov 21 17:46:58 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Thu Nov 21 17:46:58 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-qj3o2J' ==================================================================================== Thu Dec 25 00:09:59 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink01-arm64, called using "1 presto unstable /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q 0.7.2-1" as arguments. Thu Dec 25 00:09:59 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-Iur4BFZ5" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Dec 25 00:10:00 UTC 2025 I: Downloading source for unstable/presto=0.7.2-1 Reading package lists... NOTICE: 'presto' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/presto.git Please use: git clone https://salsa.debian.org/med-team/presto.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 385 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main presto 0.7.2-1 (dsc) [2233 B] Get:2 http://deb.debian.org/debian unstable/main presto 0.7.2-1 (tar) [362 kB] Get:3 http://deb.debian.org/debian unstable/main presto 0.7.2-1 (diff) [20.8 kB] Fetched 385 kB in 0s (1409 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'presto' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/presto.git Please use: git clone https://salsa.debian.org/med-team/presto.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 385 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main presto 0.7.2-1 (dsc) [2233 B] Get:2 http://deb.debian.org/debian unstable/main presto 0.7.2-1 (tar) [362 kB] Get:3 http://deb.debian.org/debian unstable/main presto 0.7.2-1 (diff) [20.8 kB] Fetched 385 kB in 0s (1409 kB/s) Download complete and in download only mode ============================================================================= Building presto in unstable on arm64 on codethink01-arm64 now. Date: Thu Dec 25 00:10:00 GMT 2025 Date UTC: Thu Dec 25 00:10:00 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Dec 24 12:10:00 -12 2025 I: pbuilder-time-stamp: 1766621400 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 [presto_0.7.2-1.dsc] I: copying [./presto_0.7.2.orig.tar.xz] I: copying [./presto_0.7.2-1.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Feb 19 12:51:18 2024 gpgv: using RSA key 4A31DB5A1EE4096C87399880903649294C33F9B7 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./presto_0.7.2-1.dsc: no acceptable signature found dpkg-source: info: extracting presto in presto-0.7.2 dpkg-source: info: unpacking presto_0.7.2.orig.tar.xz dpkg-source: info: unpacking presto_0.7.2-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2142681/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='c8405f1704b34847bbfdcd5153f53e9f' 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='2142681' 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.aBgKXB6Q/pbuilderrc_HOcn --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.aBgKXB6Q/b1 --logfile b1/build.log presto_0.7.2-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2142681/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: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all, python3-setuptools, python3-biopython, python3-pandas, python3-scipy, python3-packaging, vsearch, cd-hit dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20084 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-packaging; however: Package python3-packaging is not installed. pbuilder-satisfydepends-dummy depends on vsearch; however: Package vsearch is not installed. pbuilder-satisfydepends-dummy depends on cd-hit; however: Package cd-hit 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: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cd-hit{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{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} libxml2{a} libxrender1{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-autocommand{a} python3-biopython{a} python3-cairo{a} python3-chardet{a} python3-dateutil{a} python3-decorator{a} python3-freetype{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pkg-resources{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} vsearch{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra krb5-locales libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-bottleneck python3-bs4 python3-html5lib python3-jinja2 python3-lxml python3-matplotlib python3-numexpr python3-odf python3-olefile python3-openpyxl python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 132 newly installed, 0 to remove and 0 not upgraded. Need to get 91.9 MB of archives. After unpacking 419 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.7-3 [808 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.7-3 [1940 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.7-1 [26.8 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 12 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.7-3 [1902 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.7-1 [9708 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.7-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.0-2 [850 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.0-2 [1838 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 cd-hit arm64 4.8.1-4+b1 [509 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 48 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 62 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.2.0-1 [731 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20241024 [109 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1+b1 [22.5 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 78 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b2 [27.2 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.2-3 [1411 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b2 [25.6 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.0-2+b4 [185 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [1922 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.1-1+b2 [13.8 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libwebpdemux2 arm64 1.4.0-0.1+b1 [110 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.4.0-0.1+b1 [122 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.0-2 [730 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.12.7-1 [1052 B] Get: 115 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [3816 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 python3-pil arm64 10.4.0-1+b1 [498 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 python3-cairo arm64 1.26.1-2+b1 [130 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 121 http://deb.debian.org/debian unstable/main arm64 python3-reportlab all 4.2.5-1 [1117 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 python3-biopython arm64 1.84+dfsg-4+b1 [1644 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 python3-tz all 2024.1-2 [30.9 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-5+b1 [6028 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 python3-scipy arm64 1.13.1-6 [18.2 MB] Get: 132 http://deb.debian.org/debian unstable/main arm64 vsearch arm64 2.29.1-1 [410 kB] Fetched 91.9 MB in 1s (172 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (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 ... 20084 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.7-3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_arm64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:arm64 (3.12.7-3) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20404 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_arm64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_arm64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21466 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_arm64.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../001-libpython3.13-minimal_3.13.0-2_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../002-python3.13-minimal_3.13.0-2_arm64.deb ... Unpacking python3.13-minimal (3.13.0-2) ... Selecting previously unselected package sgml-base. Preparing to unpack .../003-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../006-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../009-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../012-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../014-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../015-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../016-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../017-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../018-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package cd-hit. Preparing to unpack .../019-cd-hit_4.8.1-4+b1_arm64.deb ... Unpacking cd-hit (4.8.1-4+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../020-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../021-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../022-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../023-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../024-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../025-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../026-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../027-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../028-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../029-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../030-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. 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Setting up libdeflate0:arm64 (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ... Setting up libcom-err2:arm64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Dec 25 00:10:27 UTC 2025. Universal Time is now: Thu Dec 25 00:10:27 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... Setting up libfontenc1:arm64 (1:1.1.8-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.82.2-3) ... No schema files found: doing nothing. Setting up libblas3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.15-1) ... Setting up libimagequant0:arm64 (2.18.0-1+b2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-2) ... Setting up autopoint (0.22.5-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libgfortran5:arm64 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:arm64 (1.4.0-0.1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:arm64 (4.5.1+git230720-5) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libopenjp2-7:arm64 (2.5.0-2+b4) ... Setting up python3.13-minimal (3.13.0-2) ... Setting up libx11-6:arm64 (2:1.8.10-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libwebpmux3:arm64 (1.4.0-0.1+b1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b2) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libwebpdemux2:arm64 (1.4.0-0.1+b1) ... Setting up libxext6:arm64 (2:1.3.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libreadline8t64:arm64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:arm64 (10.0.1-1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1+b1) ... Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1+b2) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Setting up python3.13 (3.13.0-2) ... Setting up po-debconf (1.0.21+nmu1) ... 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:arm64 (1.18.2-2) ... Setting up libraqm0:arm64 (0.10.1-1+b2) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up libpython3.12-stdlib:arm64 (3.12.7-3) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libpython3-stdlib:arm64 (3.12.7-1) ... Setting up python3 (3.12.7-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-tz (2024.1-2) ... Setting up python3-pil:arm64 (10.4.0-1+b1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.2-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-cairo (1.26.1-2+b1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-all (3.12.7-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up python3-reportlab (4.2.5-1) ... Setting up dh-python (6.20241024) ... Setting up python3-scipy (1.13.1-6) ... Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5+b1) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.84+dfsg-4+b1) ... 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/presto-0.7.2/ && 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 > ../presto_0.7.2-1_source.changes dpkg-buildpackage: info: source package presto dpkg-buildpackage: info: source version 0.7.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Lance Lin dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 dpkg-source: info: using options from presto-0.7.2/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean running clean removing '/build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it I: pybuild base:311: python3.12 setup.py clean running clean removing '/build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config running config I: pybuild base:311: python3.12 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py build running build running build_py creating /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/__init__.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Version.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Sequence.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Multiprocessing.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/IO.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Defaults.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Commandline.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Applications.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Annotation.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto running build_scripts creating build/scripts-3.13 copying and adjusting bin/AlignSets.py -> build/scripts-3.13 copying and adjusting bin/AssemblePairs.py -> build/scripts-3.13 copying and adjusting bin/BuildConsensus.py -> build/scripts-3.13 copying and adjusting bin/ClusterSets.py -> build/scripts-3.13 copying and adjusting bin/CollapseSeq.py -> build/scripts-3.13 copying and adjusting bin/ConvertHeaders.py -> build/scripts-3.13 copying and adjusting bin/EstimateError.py -> build/scripts-3.13 copying and adjusting bin/FilterSeq.py -> build/scripts-3.13 copying and adjusting bin/MaskPrimers.py -> build/scripts-3.13 copying and adjusting bin/PairSeq.py -> build/scripts-3.13 copying and adjusting bin/ParseHeaders.py -> build/scripts-3.13 copying and adjusting bin/ParseLog.py -> build/scripts-3.13 copying and adjusting bin/SplitSeq.py -> build/scripts-3.13 copying and adjusting bin/UnifyHeaders.py -> build/scripts-3.13 changing mode of build/scripts-3.13/AlignSets.py from 644 to 755 changing mode of build/scripts-3.13/AssemblePairs.py from 644 to 755 changing mode of build/scripts-3.13/BuildConsensus.py from 644 to 755 changing mode of build/scripts-3.13/ClusterSets.py from 644 to 755 changing mode of build/scripts-3.13/CollapseSeq.py from 644 to 755 changing mode of build/scripts-3.13/ConvertHeaders.py from 644 to 755 changing mode of build/scripts-3.13/EstimateError.py from 644 to 755 changing mode of build/scripts-3.13/FilterSeq.py from 644 to 755 changing mode of build/scripts-3.13/MaskPrimers.py from 644 to 755 changing mode of build/scripts-3.13/PairSeq.py from 644 to 755 changing mode of build/scripts-3.13/ParseHeaders.py from 644 to 755 changing mode of build/scripts-3.13/ParseLog.py from 644 to 755 changing mode of build/scripts-3.13/SplitSeq.py from 644 to 755 changing mode of build/scripts-3.13/UnifyHeaders.py from 644 to 755 I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/__init__.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Version.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Sequence.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Multiprocessing.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/IO.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Defaults.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Commandline.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Applications.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Annotation.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto running build_scripts creating build/scripts-3.12 copying and adjusting bin/AlignSets.py -> build/scripts-3.12 copying and adjusting bin/AssemblePairs.py -> build/scripts-3.12 copying and adjusting bin/BuildConsensus.py -> build/scripts-3.12 copying and adjusting bin/ClusterSets.py -> build/scripts-3.12 copying and adjusting bin/CollapseSeq.py -> build/scripts-3.12 copying and adjusting bin/ConvertHeaders.py -> build/scripts-3.12 copying and adjusting bin/EstimateError.py -> build/scripts-3.12 copying and adjusting bin/FilterSeq.py -> build/scripts-3.12 copying and adjusting bin/MaskPrimers.py -> build/scripts-3.12 copying and adjusting bin/PairSeq.py -> build/scripts-3.12 copying and adjusting bin/ParseHeaders.py -> build/scripts-3.12 copying and adjusting bin/ParseLog.py -> build/scripts-3.12 copying and adjusting bin/SplitSeq.py -> build/scripts-3.12 copying and adjusting bin/UnifyHeaders.py -> build/scripts-3.12 changing mode of build/scripts-3.12/AlignSets.py from 644 to 755 changing mode of build/scripts-3.12/AssemblePairs.py from 644 to 755 changing mode of build/scripts-3.12/BuildConsensus.py from 644 to 755 changing mode of build/scripts-3.12/ClusterSets.py from 644 to 755 changing mode of build/scripts-3.12/CollapseSeq.py from 644 to 755 changing mode of build/scripts-3.12/ConvertHeaders.py from 644 to 755 changing mode of build/scripts-3.12/EstimateError.py from 644 to 755 changing mode of build/scripts-3.12/FilterSeq.py from 644 to 755 changing mode of build/scripts-3.12/MaskPrimers.py from 644 to 755 changing mode of build/scripts-3.12/PairSeq.py from 644 to 755 changing mode of build/scripts-3.12/ParseHeaders.py from 644 to 755 changing mode of build/scripts-3.12/ParseLog.py from 644 to 755 changing mode of build/scripts-3.12/SplitSeq.py from 644 to 755 changing mode of build/scripts-3.12/UnifyHeaders.py from 644 to 755 dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: cp -r /build/reproducible-path/presto-0.7.2/bin /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build; I: pybuild base:311: cd /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build; python3.13 -m unittest discover -v /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Annotation.py:293: SyntaxWarning: invalid escape sequence '\s' sub_regex = '[%s\s]+' % re.escape(''.join(delimiter)) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Annotation.py:368: SyntaxWarning: invalid escape sequence '\s' sub_regex = '[%s\s]+' % re.escape(''.join(delimiter[1:])) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Annotation.py:491: SyntaxWarning: invalid escape sequence '\s' header['SPECIES'] = re.sub('\s', '_', fields[2]) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Annotation.py:493: SyntaxWarning: invalid escape sequence '\(' header['FUNCTIONALITY'] = re.sub('[\(\)\[\]]', '', fields[3]) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Annotation.py:494: SyntaxWarning: invalid escape sequence '\s' header['PARTIAL'] = 'FALSE' if re.sub('\s', '', fields[13]) == '' else 'TRUE' /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/IO.py:34: SyntaxWarning: invalid escape sequence '\s' if replace_special: parse_id = lambda x: re.sub('[\s,=|]+', '_', x) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Applications.py:61: SyntaxWarning: invalid escape sequence '\.' version = re.sub('\.linux.*$','',version) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Applications.py:288: SyntaxWarning: invalid escape sequence '\>' id_regex = re.compile('([0-9]+\t[0-9]+nt, \>)(.+)(\.\.\.)') test_collapseAnnotation (tests.test_Annotation.TestAnnotation.test_collapseAnnotation) ... ok test_getCoordKey (tests.test_Annotation.TestAnnotation.test_getCoordKey) ... ok test_mergeAnnotation (tests.test_Annotation.TestAnnotation.test_mergeAnnotation) ... ok test_renameAnnotation (tests.test_Annotation.TestAnnotation.test_renameAnnotation) ... ok test_alignAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_alignAssembly) ... skipped '-> alignAssembly() skipped\n' test_makeBlastnDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeBlastnDb) ... skipped '-> makeBlastnDb() skipped\n' test_makeUSearchDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeUSearchDb) ... skipped '-> makeUSearchDb() skipped\n' test_referenceAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_referenceAssembly) ... skipped '-> referenceAssembly() skipped\n' test_runBlastn (tests.test_AssemblePairs.TestAssemblePairs.test_runBlastn) ... skipped '-> runBlastn() skipped\n' test_runUSearch (tests.test_AssemblePairs.TestAssemblePairs.test_runUSearch) ... skipped '-> runUSearch() skipped\n' test_calculateSetError (tests.test_BuildConsensus.TestBuildConsensus.test_calculateSetError) ... ok test_deleteSeqPositions (tests.test_BuildConsensus.TestBuildConsensus.test_deleteSeqPositions) ... ok test_findGapPositions (tests.test_BuildConsensus.TestBuildConsensus.test_findGapPositions) ... ok test_frequencyConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_frequencyConsensus) ... ok test_qualityConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_qualityConsensus) ... ok test_runCDHit (tests.test_ClusterSets.TestClusterSets.test_runCDHit) ... ok test_runUClust (tests.test_ClusterSets.TestClusterSets.test_runUClust) ... ok test_checkSeqEqual (tests.test_CollapseSeq.TestCollapseSeq.test_checkSeqEqual) ... ok test_convert454Header (tests.test_ConvertHeaders.TestConvertHeaders.test_convert454Header) ... ok test_convertGenbankHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertGenbankHeader) ... ok test_convertGenericHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertGenericHeader) ... ok test_convertIMGTHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertIMGTHeader) ... ok test_convertIlluminaHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertIlluminaHeader) ... ok test_convertSRAHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertSRAHeader) ... ok test_calculateDistances (tests.test_EstimateError.TestEstimateError.test_calculateDistances) ... /usr/lib/python3/dist-packages/Bio/SeqRecord.py:228: BiopythonDeprecationWarning: Using a string as the sequence is deprecated and will raise a TypeError in future. It has been converted to a Seq object. warnings.warn( ok test_countMismatches (tests.test_EstimateError.TestEstimateError.test_countMismatches) ... ok test_initializeMismatchDictionary (tests.test_EstimateError.TestEstimateError.test_initializeMismatchDictionary) ... ok test_getFileType (tests.test_IO.TestIO.test_getFileType) ... ok test_extractAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_extractAlignment) ... ok test_localAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_localAlignment) ... -> test_collapseAnnotation() OrderedDict({'ID': 'SEQ1', 'TEST1': 'A', 'TEST2': 1, 'TEST3': 'First'}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'B', 'TEST2': 2, 'TEST3': 'Second'}) OrderedDict({'ID': 'SEQ1', 'TEST1': ['A', 'B'], 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'AB', 'TEST2': '12', 'TEST3': 'FirstSecond'}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '1', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '2', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '3', 'TEST3': ['First', 'Second']}) <- test_collapseAnnotation() 0.000 -> test_getCoordKey() ['MISEQ:132:000000000-A2F3U:1:1101:14340:1555', 'HWI-EAS209_0006_FC706VJ:5:58:5894:21141', 'MS6_33112:1:1101:18371:1066'] ['SRR001666.1', 'SRR735691.1', 'SRR1383326.1', 'SRR1383326.1', 'ERR346596.6'] ['000034_0199_0169', 'GXGJ56Z01AE06X'] <- test_getCoordKey() 0.000 -> test_mergeAnnotation() OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,C,C', 'TEST2': '1,2,3', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'C,C,A,B', 'TEST2': '3,1,2', 'TEST3': ['First', 'Second']}) <- test_mergeAnnotation() 0.000 -> test_renameAnnotation() OrderedDict({'ID': 'SEQ1', 'RENAMED1': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'RENAMED2': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2,First,Second'}) <- test_renameAnnotation() 0.000 -> test_calculateSetError() Frequency consensus error> REF> CGGCGTAA SEQ1> CGGCGTAA SEQ2> CCNNGTAA SEQ3> CGGC--TA SEQ4> CGNN--TA SEQ5> CGGC--AA ERROR> 0.250000 Quality consensus error> REF> CGGCNNAA SEQ1> CGGCGTAA SEQ2> CCNNGTAA SEQ3> CGGC--TA SEQ4> CGNN--TA SEQ5> CGGC--AA ERROR> 0.233333 <- test_calculateSetError() 0.000 -> test_deleteSeqPositions() MAX_GAP=0.4> CGGCAA MAX_GAP=0.8> CGGCGTAA <- test_deleteSeqPositions() 0.000 -> test_findGapPositions() MAX_GAP=0.4> [4, 5] MAX_GAP=0.8> [] <- test_findGapPositions() 0.000 -> test_frequencyConsensus() MIN_FREQ=0.2> CGGCGTAA MIN_FREQ=0.8> CGGCGTNA <- test_frequencyConsensus() 0.000 -> test_qualityConsensus() MIN_QUAL=0> CGGCGTAA [90, 90, 36, 36, 16, 16, 72, 90] MIN_QUAL=20> CGGCNNAA [90, 90, 36, 36, 0, 0, 72, 90] MIN_FREQ=0.8> CGGCNNNA [90, 90, 36, 36, 0, 0, 0, 90] <- test_qualityConsensus() 0.000 -> test_runCDHit() FULL_LENGTH> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} TRIMMED> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} ZERO_LENGTH> None <- test_runCDHit() 0.029 -> test_runUClust() FULL_LENGTH> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} TRIMMED> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} ZERO_LENGTH> None <- test_runUClust() 0.025 -> test_checkSeqEqual() DNA Equality> SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA EQUAL> True SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA SEQ3|COUNT=3> CCACGTTTTACTAATTAATA EQUAL> False SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA SEQ4|COUNT=4> CCACGTTTTANTAATTAATA EQUAL> True SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA SEQ3|COUNT=3> CCACGTTTTACTAATTAATA EQUAL> False SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA SEQ4|COUNT=4> CCACGTTTTANTAATTAATA EQUAL> True SEQ3|COUNT=3> CCACGTTTTACTAATTAATA SEQ4|COUNT=4> CCACGTTTTANTAATTAATA EQUAL> True <- test_checkSeqEqual() 0.000 -> test_convert454Header() OrderedDict({'ID': '000034_0199_0169', 'LENGTH': '437', 'UACCNO': 'GNDG01201ARRCR'}) OrderedDict({'ID': 'GXGJ56Z01AE06X', 'LENGTH': '222'}) <- test_convert454Header() 0.000 -> test_convertGenbankHeader() OrderedDict({'ID': 'CM000663.2', 'GI': '568336023', 'SOURCE': 'gb', 'DESC': 'Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) OrderedDict({'ID': 'CM000663.2', 'DESC': 'Homo_sapiens_chromosome_1__GRCh38_reference_primary_assembly'}) <- test_convertGenbankHeader() 0.000 -> test_convertGenericHeader() OrderedDict({'ID': 'gi_568336023_gb_CM000663.2_Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) OrderedDict({'ID': 'CM000663.2_Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) OrderedDict({'ID': 'M99641_IGHV1-18*01_Homo_sapiens_F_V-REGION_188..483_296_nt_1_296+24_320_'}) OrderedDict({'ID': "Z29978_IGHV1-69*07_Homo_sapiens_F_V-REGION_1..233_233_nt_1_233+58_291_partial_in_5'_and_in_3'_"}) OrderedDict({'ID': 'AB019439_IGHV(III)-22-2*01_Homo_sapiens_P_L-PART1+V-EXON_168065..168119+168222..168262_96_nt_1_96+0_96_'}) OrderedDict({'ID': 'AE000659_TRAV11*01_Homo_sapiens_(P)_V-REGION_85121..85397_276_nt_1_276+42_318_'}) <- test_convertGenericHeader() 0.000 -> test_convertIMGTHeader() OrderedDict({'ID': 'IGHV1-18*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'F', 'PARTIAL': 'FALSE', 'ACCESSION': 'M99641'}) OrderedDict({'ID': 'IGHV1-69*07', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'F', 'PARTIAL': 'TRUE', 'ACCESSION': 'Z29978'}) OrderedDict({'ID': 'IGHV(III)-22-2*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'L-PART1+V-EXON', 'FUNCTIONALITY': 'P', 'PARTIAL': 'FALSE', 'ACCESSION': 'AB019439'}) OrderedDict({'ID': 'TRAV11*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'P', 'PARTIAL': 'FALSE', 'ACCESSION': 'AE000659'}) OrderedDict({'ID': 'IGHV1-18*01'}) OrderedDict({'ID': 'IGHV1-69*07'}) OrderedDict({'ID': 'IGHV(III)-22-2*01'}) OrderedDict({'ID': 'TRAV11*01'}) <- test_convertIMGTHeader() 0.000 -> test_convertIlluminaHeader() OrderedDict({'ID': 'MISEQ:132:000000000-A2F3U:1:1101:14340:1555', 'INDEX': 'ATCACG', 'READ': '1'}) OrderedDict({'ID': 'HWI-EAS209_0006_FC706VJ:5:58:5894:21141', 'INDEX': 'ATCACG', 'READ': '1'}) OrderedDict({'ID': 'MS6_33112:1:1101:18371:1066', 'READ': '1'}) <- test_convertIlluminaHeader() 0.000 -> test_convertSRAHeader() OrderedDict({'ID': 'SRR001666.1', 'DESC': '071112_SLXA-EAS1_s_7:5:1:817:345', 'LENGTH': '36'}) OrderedDict({'ID': 'SRR735691.1', 'DESC': 'GXGJ56Z01AE06X', 'LENGTH': '222'}) OrderedDict({'ID': 'SRR1383326.1', 'DESC': '1', 'LENGTH': '250'}) OrderedDict({'ID': 'SRR1383326.1', 'READ': '2', 'DESC': '1', 'LENGTH': '250'}) OrderedDict({'ID': 'ERR346596.6', 'DESC': 'BS-DSFCONTROL04:4:000000000-A3F0Y:1:1101:13220:1649/1'}) <- test_convertSRAHeader() 0.000 -> test_calculateDistances() <- test_calculateDistances() 0.002 -> test_countMismatches() <- test_countMismatches() 0.001 -> test_initializeMismatchDictionary() <- test_initializeMismatchDictionary() 0.000 -> test_getFileType() <- test_getFileType() 0.000 -> test_extractAlignment() SEQ1> SEQ> CCACGTTTTAGTAATTAATA ALN-SEQ> CCACGTTTTAGT ALN-PR> ----GTTTTAGT PRIMER> GTTTTAGT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ2> SEQ> CCNCGTTTTAGTAATTAATA ALN-SEQ> CCNCGTTTTAGT ALN-PR> ----GTTTTAGT PRIMER> GTTTTAGT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ3> SEQ> GGGCGTTTTAGTAATTAATA ALN-SEQ> GGGCGTTTTAGT ALN-PR> ----GTTTTAGT PRIMER> GTTTTAGT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTTACT ALN-PR> ----GTTTTACT PRIMER> GTTTTACT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNNACT ALN-PR> ----NNNNNACT PRIMER> NNNNNACT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNNACT ALN-PR> ----TANNNACT PRIMER> TANNNACT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> NNNNNNNNNNNN ALN-PR> ----NNNNNNNN PRIMER> NNNNNNNN START> 4 END> 12 GAPS> 0 ERROR> 0.000000 <- test_extractAlignment() 0.000 -> test_localAlignment() TEST Ns> SEQ1> SEQ> CCACGTTTTAGTAATTAATA ALN-SEQ> CCACGTTTTAGTAATTAATA ALN-PR> -CACGTTTT----------- PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ2> SEQ> CCNCGTTTTAGTAATTAATA ALN-SEQ> CCNCGTTTTAGTAATTAATA ALN-PR> -CACGTTTT----------- PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.125000 ok test_maskSeq (tests.test_MaskPrimers.TestMaskPrimers.test_maskSeq) ... ok test_scoreAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_scoreAlignment) ... ok test_calculateSetError (tests.test_Sequence.TestSequence.test_calculateSetError) ... ok test_filterQuality (tests.test_Sequence.TestSequence.test_filterQuality) ... ok test_meanQuality (tests.test_Sequence.TestSequence.test_meanQuality) ... ok test_scoreDNA (tests.test_Sequence.TestSequence.test_scoreDNA) ... ok test_scoreSeqPair (tests.test_Sequence.TestSequence.test_scoreSeqPair) ... SEQ3> SEQ> GGGCGTTTTAGTAATTAATA ALN-SEQ> GGGCGTTTTAGTAATTAATA ALN-PR> -GGCGTTTT----------- PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTTACTAATTAATA ALN-PR> GGC-GTTTT----------- PRIMER> PR2 START> 0 END> 9 GAPS> 1 ERROR> 0.250000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNNACTAATTAATA ALN-PR> ------------ANATAA-- PRIMER> PR3 START> 12 END> 18 GAPS> 0 ERROR> 0.375000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNNACTAATTAATA ALN-PR> -GGANA-------------- PRIMER> PR3 START> 1 END> 6 GAPS> 0 ERROR> 0.375000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> None ALN-PR> None PRIMER> None START> None END> None GAPS> 0 ERROR> 1.000000 TEST INDELS> SEQ1> SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG ALN-SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG ALN-PR> ---------------ATACGTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 15 END> 38 GAPS> 0 ERROR> 0.083333 SEQ2> SEQ> CGGATCTTCTACTCAAAACCGTCCTCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG ALN-SEQ> CGGATCTTCTACTCAAAACCGTCC-TCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG ALN-PR> --------------AATAC-GTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 14 END> 38 GAPS> 2 ERROR> 0.208333 SEQ3> SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTGATCTGTTTTACATGGGGGCATCACCCAG ALN-SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTG-ATCTGTTTTACATGGGGGCATCACCCAG ALN-PR> ---------------AATACGTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 15 END> 38 GAPS> 1 ERROR> 0.125000 SEQ4> SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT ALN-SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT ALN-PR> ------CATCT-TCCTCTA------------------------------------------- PRIMER> PR2 START> 6 END> 19 GAPS> 1 ERROR> 0.250000 SEQ5> SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG ALN-SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG ALN-PR> ------CATCTTCCTCTA-------------------------------------------- PRIMER> PR2 START> 6 END> 18 GAPS> 0 ERROR> 0.166667 SEQ6> SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA ALN-SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA ALN-PR> TCT-TCCTCTA--------------------------------------------------- PRIMER> PR2 START> 0 END> 11 GAPS> 1 ERROR> 0.250000 SEQ7> SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> --GTGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 2 END> 15 GAPS> 1 ERROR> 0.083333 SEQ8> SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 3 END> 15 GAPS> 1 ERROR> 0.166667 SEQ9> SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 3 END> 15 GAPS> 1 ERROR> 0.333333 SEQ10> SEQ> -------------------------------------------------------------- ALN-SEQ> None ALN-PR> None PRIMER> None START> None END> None GAPS> 0 ERROR> 1.000000 <- test_localAlignment() 0.028 -> test_maskSeq() TEST CUT> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> AGTAATTAATA TEST MASK> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> NNNNNNAGTAATTAATA TEST TRIM> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> CGTTTTAGTAATTAATA TEST TAG> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> CCACGTTTTAGTAATTAATA <- test_maskSeq() 0.001 -> test_scoreAlignment() SEQ1> SEQ> CCACGTTTTAGTAATTAATA ALN-SEQ> CCACGTTTT ALN-PR> -CACGTTTT PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ2> SEQ> CCNCGTTTTAGTAATTAATA ALN-SEQ> CCNCGTTTT ALN-PR> -CACGTTTT PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.125000 SEQ3> SEQ> GGGCGTTTTAGTAATTAATA ALN-SEQ> GGGCGTTTT ALN-PR> -GGCGTTTT PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTT ALN-PR> -GGCGTTTT PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.250000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNN ALN-PR> -GGCGTTTT PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.750000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNN ALN-PR> -GGANATAA PRIMER> PR3 START> 1 END> 9 GAPS> 0 ERROR> 0.375000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> NNNNNNNNN ALN-PR> -CACGTTTT PRIMER> None START> 1 END> 9 GAPS> 0 ERROR> 1.000000 <- test_scoreAlignment() 0.007 -> test_calculateSetError() REF> CGGCGTAA 0.4347826086956522 REF> NNNNNNNN 1.0 <- test_calculateSetError() 0.000 -> test_filterQuality() RESULT> True 25 RESULT> False 5 RESULT> False 0 <- test_filterQuality() 0.000 -> test_meanQuality() RESULT> 25 [30, 30, 20, 20, 30, 30, 40, 40] RESULT> 5 [30, 30, 0, 0, 30, 30, 20, 20] RESULT> 0 [0, 0, 0, 0, 0, 0, 0, 0] <- test_meanQuality() 0.000 -> test_scoreDNA() Default DNA Scores> A==A> 1 A==T> 0 A==R> 1 U==T> 1 A==N> 1 N==A> 1 A==-> 0 -==A> 0 Symmetric DNA Scores> A==A> 1 A==T> 0 A==R> 1 U==T> 1 A==N> 1 N==A> 1 A==-> 1 -==A> 1 Asymmetric DNA Scores> A==A> 1 A==T> 0 A==R> 1 U==T> 1 A==N> 1 N==A> 0 A==-> 1 -==A> 0 <- test_scoreDNA() 0.000 -> test_scoreSeqPair() Default DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ6> NNNNNNAA SEQ7> --------ok test_weightDNA (tests.test_Sequence.TestSequence.test_weightDNA) ... ok test_consensusUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_consensusUnify) ... ok test_deletionUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_deletionUnify) ... ok ---------------------------------------------------------------------- Ran 40 tests in 0.110s OK (skipped=6) SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ7> -------- SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 Asymmetric DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 3 WEIGHT> 8 ERROR> 0.625000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ7> -------- SEQ8> CG------ SCORE> 0 WEIGHT> 8 ERROR> 1.000000 Masked DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 5 WEIGHT> 6 ERROR> 0.166667 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 3 WEIGHT> 6 ERROR> 0.500000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 2 WEIGHT> 2 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 3 WEIGHT> 6 ERROR> 0.500000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 4 WEIGHT> 6 ERROR> 0.333333 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 1 WEIGHT> 2 ERROR> 0.500000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 0 WEIGHT> 6 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 2 WEIGHT> 6 ERROR> 0.666667 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 6 ERROR> 0.166667 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 2 WEIGHT> 2 ERROR> 0.000000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 1 WEIGHT> 2 ERROR> 0.500000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 2 WEIGHT> 6 ERROR> 0.666667 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 6 ERROR> 0.333333 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ7> -------- SCORE> 0 WEIGHT> 2 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 0 WEIGHT> 2 ERROR> 1.000000 SEQ7> -------- SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 <- test_scoreSeqPair() 0.006 -> test_weightDNA() DNA Weight> SEQ1> 8 SEQ2> 6 SEQ3> 8 SEQ4> 6 SEQ5> 0 SEQ6> 2 SEQ7> 8 SEQ8> 8 AA Weight> SEQ1> 8 SEQ2> 6 SEQ3> 8 SEQ4> 6 <- test_weightDNA() 0.000 -> test_consensusUnify() ID> SEQ0|BARCODE=AAAA|SAMPLE=S1 -> SEQ0|BARCODE=AAAA|SAMPLE=S1 ID> SEQ1|BARCODE=AAAA|SAMPLE=S1 -> SEQ1|BARCODE=AAAA|SAMPLE=S1 ID> SEQ2|BARCODE=AAAA|SAMPLE=S2 -> SEQ2|BARCODE=AAAA|SAMPLE=S1 ID> SEQ3|BARCODE=AAAA|SAMPLE=S3 -> SEQ3|BARCODE=AAAA|SAMPLE=S1 ID> SEQ4|BARCODE=CCCC|SAMPLE=S1 -> SEQ4|BARCODE=CCCC|SAMPLE=S1 ID> SEQ5|BARCODE=CCCC|SAMPLE=S2 -> SEQ5|BARCODE=CCCC|SAMPLE=S1 ID> SEQ6|BARCODE=GGGG|SAMPLE=S2 -> SEQ6|BARCODE=GGGG|SAMPLE=S2 ID> SEQ7|BARCODE=GGGG|SAMPLE=S2 -> SEQ7|BARCODE=GGGG|SAMPLE=S2 <- test_consensusUnify() 0.000 -> test_deletionUnify() ID> SEQ0|BARCODE=AAAA|SAMPLE=S1 -> False ID> SEQ1|BARCODE=AAAA|SAMPLE=S1 -> False ID> SEQ2|BARCODE=AAAA|SAMPLE=S2 -> False ID> SEQ3|BARCODE=AAAA|SAMPLE=S3 -> False ID> SEQ4|BARCODE=CCCC|SAMPLE=S1 -> False ID> SEQ5|BARCODE=CCCC|SAMPLE=S2 -> False ID> SEQ6|BARCODE=GGGG|SAMPLE=S2 -> True ID> SEQ7|BARCODE=GGGG|SAMPLE=S2 -> True <- test_deletionUnify() 0.000 I: pybuild pybuild:308: cp -r /build/reproducible-path/presto-0.7.2/bin /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build; I: pybuild base:311: cd /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build; python3.12 -m unittest discover -v /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:293: SyntaxWarning: invalid escape sequence '\s' sub_regex = '[%s\s]+' % re.escape(''.join(delimiter)) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:368: SyntaxWarning: invalid escape sequence '\s' sub_regex = '[%s\s]+' % re.escape(''.join(delimiter[1:])) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:491: SyntaxWarning: invalid escape sequence '\s' header['SPECIES'] = re.sub('\s', '_', fields[2]) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:493: SyntaxWarning: invalid escape sequence '\(' header['FUNCTIONALITY'] = re.sub('[\(\)\[\]]', '', fields[3]) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:494: SyntaxWarning: invalid escape sequence '\s' header['PARTIAL'] = 'FALSE' if re.sub('\s', '', fields[13]) == '' else 'TRUE' /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/IO.py:34: SyntaxWarning: invalid escape sequence '\s' if replace_special: parse_id = lambda x: re.sub('[\s,=|]+', '_', x) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Applications.py:61: SyntaxWarning: invalid escape sequence '\.' version = re.sub('\.linux.*$','',version) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Applications.py:288: SyntaxWarning: invalid escape sequence '\>' id_regex = re.compile('([0-9]+\t[0-9]+nt, \>)(.+)(\.\.\.)') test_collapseAnnotation (tests.test_Annotation.TestAnnotation.test_collapseAnnotation) ... ok test_getCoordKey (tests.test_Annotation.TestAnnotation.test_getCoordKey) ... ok test_mergeAnnotation (tests.test_Annotation.TestAnnotation.test_mergeAnnotation) ... ok test_renameAnnotation (tests.test_Annotation.TestAnnotation.test_renameAnnotation) ... ok test_alignAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_alignAssembly) ... skipped '-> alignAssembly() skipped\n' test_makeBlastnDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeBlastnDb) ... skipped '-> makeBlastnDb() skipped\n' test_makeUSearchDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeUSearchDb) ... skipped '-> makeUSearchDb() skipped\n' test_referenceAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_referenceAssembly) ... skipped '-> referenceAssembly() skipped\n' test_runBlastn (tests.test_AssemblePairs.TestAssemblePairs.test_runBlastn) ... skipped '-> runBlastn() skipped\n' test_runUSearch (tests.test_AssemblePairs.TestAssemblePairs.test_runUSearch) ... skipped '-> runUSearch() skipped\n' test_calculateSetError (tests.test_BuildConsensus.TestBuildConsensus.test_calculateSetError) ... ok test_deleteSeqPositions (tests.test_BuildConsensus.TestBuildConsensus.test_deleteSeqPositions) ... ok test_findGapPositions (tests.test_BuildConsensus.TestBuildConsensus.test_findGapPositions) ... ok test_frequencyConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_frequencyConsensus) ... ok test_qualityConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_qualityConsensus) ... ok test_runCDHit (tests.test_ClusterSets.TestClusterSets.test_runCDHit) ... ok test_runUClust (tests.test_ClusterSets.TestClusterSets.test_runUClust) ... ok test_checkSeqEqual (tests.test_CollapseSeq.TestCollapseSeq.test_checkSeqEqual) ... ok test_convert454Header (tests.test_ConvertHeaders.TestConvertHeaders.test_convert454Header) ... ok test_convertGenbankHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertGenbankHeader) ... ok test_convertGenericHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertGenericHeader) ... ok test_convertIMGTHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertIMGTHeader) ... ok test_convertIlluminaHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertIlluminaHeader) ... ok test_convertSRAHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertSRAHeader) ... ok test_calculateDistances (tests.test_EstimateError.TestEstimateError.test_calculateDistances) ... /usr/lib/python3/dist-packages/Bio/SeqRecord.py:228: BiopythonDeprecationWarning: Using a string as the sequence is deprecated and will raise a TypeError in future. It has been converted to a Seq object. warnings.warn( ok test_countMismatches (tests.test_EstimateError.TestEstimateError.test_countMismatches) ... ok test_initializeMismatchDictionary (tests.test_EstimateError.TestEstimateError.test_initializeMismatchDictionary) ... ok test_getFileType (tests.test_IO.TestIO.test_getFileType) ... ok test_extractAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_extractAlignment) ... ok test_localAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_localAlignment) ... -> test_collapseAnnotation() OrderedDict({'ID': 'SEQ1', 'TEST1': 'A', 'TEST2': 1, 'TEST3': 'First'}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'B', 'TEST2': 2, 'TEST3': 'Second'}) OrderedDict({'ID': 'SEQ1', 'TEST1': ['A', 'B'], 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'AB', 'TEST2': '12', 'TEST3': 'FirstSecond'}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '1', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '2', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '3', 'TEST3': ['First', 'Second']}) <- test_collapseAnnotation() 0.000 -> test_getCoordKey() ['MISEQ:132:000000000-A2F3U:1:1101:14340:1555', 'HWI-EAS209_0006_FC706VJ:5:58:5894:21141', 'MS6_33112:1:1101:18371:1066'] ['SRR001666.1', 'SRR735691.1', 'SRR1383326.1', 'SRR1383326.1', 'ERR346596.6'] ['000034_0199_0169', 'GXGJ56Z01AE06X'] <- test_getCoordKey() 0.000 -> test_mergeAnnotation() OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,C,C', 'TEST2': '1,2,3', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'C,C,A,B', 'TEST2': '3,1,2', 'TEST3': ['First', 'Second']}) <- test_mergeAnnotation() 0.000 -> test_renameAnnotation() OrderedDict({'ID': 'SEQ1', 'RENAMED1': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'RENAMED2': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2,First,Second'}) <- test_renameAnnotation() 0.000 -> test_calculateSetError() Frequency consensus error> REF> CGGCGTAA SEQ1> CGGCGTAA SEQ2> CCNNGTAA SEQ3> CGGC--TA SEQ4> CGNN--TA SEQ5> CGGC--AA ERROR> 0.250000 Quality consensus error> REF> CGGCNNAA SEQ1> CGGCGTAA SEQ2> CCNNGTAA SEQ3> CGGC--TA SEQ4> CGNN--TA SEQ5> CGGC--AA ERROR> 0.233333 <- test_calculateSetError() 0.000 -> test_deleteSeqPositions() MAX_GAP=0.4> CGGCAA MAX_GAP=0.8> CGGCGTAA <- test_deleteSeqPositions() 0.000 -> test_findGapPositions() MAX_GAP=0.4> [4, 5] MAX_GAP=0.8> [] <- test_findGapPositions() 0.000 -> test_frequencyConsensus() MIN_FREQ=0.2> CGGCGTAA MIN_FREQ=0.8> CGGCGTNA <- test_frequencyConsensus() 0.000 -> test_qualityConsensus() MIN_QUAL=0> CGGCGTAA [90, 90, 36, 36, 16, 16, 72, 90] MIN_QUAL=20> CGGCNNAA [90, 90, 36, 36, 0, 0, 72, 90] MIN_FREQ=0.8> CGGCNNNA [90, 90, 36, 36, 0, 0, 0, 90] <- test_qualityConsensus() 0.000 -> test_runCDHit() FULL_LENGTH> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} TRIMMED> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} ZERO_LENGTH> None <- test_runCDHit() 0.016 -> test_runUClust() FULL_LENGTH> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} TRIMMED> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} ZERO_LENGTH> None <- test_runUClust() 0.027 -> test_checkSeqEqual() DNA Equality> SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA EQUAL> True SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA SEQ3|COUNT=3> CCACGTTTTACTAATTAATA EQUAL> False SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA SEQ4|COUNT=4> CCACGTTTTANTAATTAATA EQUAL> True SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA SEQ3|COUNT=3> CCACGTTTTACTAATTAATA EQUAL> False SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA SEQ4|COUNT=4> CCACGTTTTANTAATTAATA EQUAL> True SEQ3|COUNT=3> CCACGTTTTACTAATTAATA SEQ4|COUNT=4> CCACGTTTTANTAATTAATA EQUAL> True <- test_checkSeqEqual() 0.000 -> test_convert454Header() OrderedDict({'ID': '000034_0199_0169', 'LENGTH': '437', 'UACCNO': 'GNDG01201ARRCR'}) OrderedDict({'ID': 'GXGJ56Z01AE06X', 'LENGTH': '222'}) <- test_convert454Header() 0.000 -> test_convertGenbankHeader() OrderedDict({'ID': 'CM000663.2', 'GI': '568336023', 'SOURCE': 'gb', 'DESC': 'Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) OrderedDict({'ID': 'CM000663.2', 'DESC': 'Homo_sapiens_chromosome_1__GRCh38_reference_primary_assembly'}) <- test_convertGenbankHeader() 0.000 -> test_convertGenericHeader() OrderedDict({'ID': 'gi_568336023_gb_CM000663.2_Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) OrderedDict({'ID': 'CM000663.2_Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) OrderedDict({'ID': 'M99641_IGHV1-18*01_Homo_sapiens_F_V-REGION_188..483_296_nt_1_296+24_320_'}) OrderedDict({'ID': "Z29978_IGHV1-69*07_Homo_sapiens_F_V-REGION_1..233_233_nt_1_233+58_291_partial_in_5'_and_in_3'_"}) OrderedDict({'ID': 'AB019439_IGHV(III)-22-2*01_Homo_sapiens_P_L-PART1+V-EXON_168065..168119+168222..168262_96_nt_1_96+0_96_'}) OrderedDict({'ID': 'AE000659_TRAV11*01_Homo_sapiens_(P)_V-REGION_85121..85397_276_nt_1_276+42_318_'}) <- test_convertGenericHeader() 0.000 -> test_convertIMGTHeader() OrderedDict({'ID': 'IGHV1-18*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'F', 'PARTIAL': 'FALSE', 'ACCESSION': 'M99641'}) OrderedDict({'ID': 'IGHV1-69*07', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'F', 'PARTIAL': 'TRUE', 'ACCESSION': 'Z29978'}) OrderedDict({'ID': 'IGHV(III)-22-2*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'L-PART1+V-EXON', 'FUNCTIONALITY': 'P', 'PARTIAL': 'FALSE', 'ACCESSION': 'AB019439'}) OrderedDict({'ID': 'TRAV11*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'P', 'PARTIAL': 'FALSE', 'ACCESSION': 'AE000659'}) OrderedDict({'ID': 'IGHV1-18*01'}) OrderedDict({'ID': 'IGHV1-69*07'}) OrderedDict({'ID': 'IGHV(III)-22-2*01'}) OrderedDict({'ID': 'TRAV11*01'}) <- test_convertIMGTHeader() 0.000 -> test_convertIlluminaHeader() OrderedDict({'ID': 'MISEQ:132:000000000-A2F3U:1:1101:14340:1555', 'INDEX': 'ATCACG', 'READ': '1'}) OrderedDict({'ID': 'HWI-EAS209_0006_FC706VJ:5:58:5894:21141', 'INDEX': 'ATCACG', 'READ': '1'}) OrderedDict({'ID': 'MS6_33112:1:1101:18371:1066', 'READ': '1'}) <- test_convertIlluminaHeader() 0.000 -> test_convertSRAHeader() OrderedDict({'ID': 'SRR001666.1', 'DESC': '071112_SLXA-EAS1_s_7:5:1:817:345', 'LENGTH': '36'}) OrderedDict({'ID': 'SRR735691.1', 'DESC': 'GXGJ56Z01AE06X', 'LENGTH': '222'}) OrderedDict({'ID': 'SRR1383326.1', 'DESC': '1', 'LENGTH': '250'}) OrderedDict({'ID': 'SRR1383326.1', 'READ': '2', 'DESC': '1', 'LENGTH': '250'}) OrderedDict({'ID': 'ERR346596.6', 'DESC': 'BS-DSFCONTROL04:4:000000000-A3F0Y:1:1101:13220:1649/1'}) <- test_convertSRAHeader() 0.000 -> test_calculateDistances() <- test_calculateDistances() 0.001 -> test_countMismatches() <- test_countMismatches() 0.001 -> test_initializeMismatchDictionary() <- test_initializeMismatchDictionary() 0.000 -> test_getFileType() <- test_getFileType() 0.000 -> test_extractAlignment() SEQ1> SEQ> CCACGTTTTAGTAATTAATA ALN-SEQ> CCACGTTTTAGT ALN-PR> ----GTTTTAGT PRIMER> GTTTTAGT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ2> SEQ> CCNCGTTTTAGTAATTAATA ALN-SEQ> CCNCGTTTTAGT ALN-PR> ----GTTTTAGT PRIMER> GTTTTAGT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ3> SEQ> GGGCGTTTTAGTAATTAATA ALN-SEQ> GGGCGTTTTAGT ALN-PR> ----GTTTTAGT PRIMER> GTTTTAGT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTTACT ALN-PR> ----GTTTTACT PRIMER> GTTTTACT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNNACT ALN-PR> ----NNNNNACT PRIMER> NNNNNACT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNNACT ALN-PR> ----TANNNACT PRIMER> TANNNACT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> NNNNNNNNNNNN ALN-PR> ----NNNNNNNN PRIMER> NNNNNNNN START> 4 END> 12 GAPS> 0 ERROR> 0.000000 <- test_extractAlignment() 0.000 -> test_localAlignment() TEST Ns> SEQ1> SEQ> CCACGTTTTAGTAATTAATA ALN-SEQ> CCACGTTTTAGTAATTAATA ALN-PR> -CACGTTTT----------- PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ2> SEQ> CCNCGTTTTAGTAATTAATA ALN-SEQ> CCNCGTTTTAGTAATTAATA ALN-PR> -CACGTTTT----------- PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.125000 ok test_maskSeq (tests.test_MaskPrimers.TestMaskPrimers.test_maskSeq) ... ok test_scoreAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_scoreAlignment) ... ok test_calculateSetError (tests.test_Sequence.TestSequence.test_calculateSetError) ... ok test_filterQuality (tests.test_Sequence.TestSequence.test_filterQuality) ... ok test_meanQuality (tests.test_Sequence.TestSequence.test_meanQuality) ... ok test_scoreDNA (tests.test_Sequence.TestSequence.test_scoreDNA) ... ok test_scoreSeqPair (tests.test_Sequence.TestSequence.test_scoreSeqPair) ... SEQ3> SEQ> GGGCGTTTTAGTAATTAATA ALN-SEQ> GGGCGTTTTAGTAATTAATA ALN-PR> -GGCGTTTT----------- PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTTACTAATTAATA ALN-PR> GGC-GTTTT----------- PRIMER> PR2 START> 0 END> 9 GAPS> 1 ERROR> 0.250000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNNACTAATTAATA ALN-PR> ------------ANATAA-- PRIMER> PR3 START> 12 END> 18 GAPS> 0 ERROR> 0.375000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNNACTAATTAATA ALN-PR> -GGANA-------------- PRIMER> PR3 START> 1 END> 6 GAPS> 0 ERROR> 0.375000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> None ALN-PR> None PRIMER> None START> None END> None GAPS> 0 ERROR> 1.000000 TEST INDELS> SEQ1> SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG ALN-SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG ALN-PR> ---------------ATACGTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 15 END> 38 GAPS> 0 ERROR> 0.083333 SEQ2> SEQ> CGGATCTTCTACTCAAAACCGTCCTCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG ALN-SEQ> CGGATCTTCTACTCAAAACCGTCC-TCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG ALN-PR> --------------AATAC-GTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 14 END> 38 GAPS> 2 ERROR> 0.208333 SEQ3> SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTGATCTGTTTTACATGGGGGCATCACCCAG ALN-SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTG-ATCTGTTTTACATGGGGGCATCACCCAG ALN-PR> ---------------AATACGTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 15 END> 38 GAPS> 1 ERROR> 0.125000 SEQ4> SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT ALN-SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT ALN-PR> ------CATCT-TCCTCTA------------------------------------------- PRIMER> PR2 START> 6 END> 19 GAPS> 1 ERROR> 0.250000 SEQ5> SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG ALN-SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG ALN-PR> ------CATCTTCCTCTA-------------------------------------------- PRIMER> PR2 START> 6 END> 18 GAPS> 0 ERROR> 0.166667 SEQ6> SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA ALN-SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA ALN-PR> TCT-TCCTCTA--------------------------------------------------- PRIMER> PR2 START> 0 END> 11 GAPS> 1 ERROR> 0.250000 SEQ7> SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> --GTGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 2 END> 15 GAPS> 1 ERROR> 0.083333 SEQ8> SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 3 END> 15 GAPS> 1 ERROR> 0.166667 SEQ9> SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 3 END> 15 GAPS> 1 ERROR> 0.333333 SEQ10> SEQ> -------------------------------------------------------------- ALN-SEQ> None ALN-PR> None PRIMER> None START> None END> None GAPS> 0 ERROR> 1.000000 <- test_localAlignment() 0.024 -> test_maskSeq() TEST CUT> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> AGTAATTAATA TEST MASK> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> NNNNNNAGTAATTAATA TEST TRIM> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> CGTTTTAGTAATTAATA TEST TAG> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> CCACGTTTTAGTAATTAATA <- test_maskSeq() 0.001 -> test_scoreAlignment() SEQ1> SEQ> CCACGTTTTAGTAATTAATA ALN-SEQ> CCACGTTTT ALN-PR> -CACGTTTT PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ2> SEQ> CCNCGTTTTAGTAATTAATA ALN-SEQ> CCNCGTTTT ALN-PR> -CACGTTTT PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.125000 SEQ3> SEQ> GGGCGTTTTAGTAATTAATA ALN-SEQ> GGGCGTTTT ALN-PR> -GGCGTTTT PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTT ALN-PR> -GGCGTTTT PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.250000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNN ALN-PR> -GGCGTTTT PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.750000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNN ALN-PR> -GGANATAA PRIMER> PR3 START> 1 END> 9 GAPS> 0 ERROR> 0.375000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> NNNNNNNNN ALN-PR> -CACGTTTT PRIMER> None START> 1 END> 9 GAPS> 0 ERROR> 1.000000 <- test_scoreAlignment() 0.007 -> test_calculateSetError() REF> CGGCGTAA 0.4347826086956522 REF> NNNNNNNN 1.0 <- test_calculateSetError() 0.000 -> test_filterQuality() RESULT> True 25 RESULT> False 5 RESULT> False 0 <- test_filterQuality() 0.000 -> test_meanQuality() RESULT> 25 [30, 30, 20, 20, 30, 30, 40, 40] RESULT> 5 [30, 30, 0, 0, 30, 30, 20, 20] RESULT> 0 [0, 0, 0, 0, 0, 0, 0, 0] <- test_meanQuality() 0.000 -> test_scoreDNA() Default DNA Scores> A==A> 1 A==T> 0 A==R> 1 U==T> 1 A==N> 1 N==A> 1 A==-> 0 -==A> 0 Symmetric DNA Scores> A==A> 1 A==T> 0 A==R> 1 U==T> 1 A==N> 1 N==A> 1 A==-> 1 -==A> 1 Asymmetric DNA Scores> A==A> 1 A==T> 0 A==R> 1 U==T> 1 A==N> 1 N==A> 0 A==-> 1 -==A> 0 <- test_scoreDNA() 0.000 -> test_scoreSeqPair() Default DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ6> NNNNNNAA SEQ7> --------ok test_weightDNA (tests.test_Sequence.TestSequence.test_weightDNA) ... ok test_consensusUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_consensusUnify) ... ok test_deletionUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_deletionUnify) ... ok ---------------------------------------------------------------------- Ran 40 tests in 0.097s OK (skipped=6) SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ7> -------- SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 Asymmetric DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 3 WEIGHT> 8 ERROR> 0.625000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ7> -------- SEQ8> CG------ SCORE> 0 WEIGHT> 8 ERROR> 1.000000 Masked DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 5 WEIGHT> 6 ERROR> 0.166667 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 3 WEIGHT> 6 ERROR> 0.500000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 2 WEIGHT> 2 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 3 WEIGHT> 6 ERROR> 0.500000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 4 WEIGHT> 6 ERROR> 0.333333 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 1 WEIGHT> 2 ERROR> 0.500000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 0 WEIGHT> 6 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 2 WEIGHT> 6 ERROR> 0.666667 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 6 ERROR> 0.166667 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 2 WEIGHT> 2 ERROR> 0.000000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 1 WEIGHT> 2 ERROR> 0.500000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 2 WEIGHT> 6 ERROR> 0.666667 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 6 ERROR> 0.333333 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ7> -------- SCORE> 0 WEIGHT> 2 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 0 WEIGHT> 2 ERROR> 1.000000 SEQ7> -------- SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 <- test_scoreSeqPair() 0.006 -> test_weightDNA() DNA Weight> SEQ1> 8 SEQ2> 6 SEQ3> 8 SEQ4> 6 SEQ5> 0 SEQ6> 2 SEQ7> 8 SEQ8> 8 AA Weight> SEQ1> 8 SEQ2> 6 SEQ3> 8 SEQ4> 6 <- test_weightDNA() 0.000 -> test_consensusUnify() ID> SEQ0|BARCODE=AAAA|SAMPLE=S1 -> SEQ0|BARCODE=AAAA|SAMPLE=S1 ID> SEQ1|BARCODE=AAAA|SAMPLE=S1 -> SEQ1|BARCODE=AAAA|SAMPLE=S1 ID> SEQ2|BARCODE=AAAA|SAMPLE=S2 -> SEQ2|BARCODE=AAAA|SAMPLE=S1 ID> SEQ3|BARCODE=AAAA|SAMPLE=S3 -> SEQ3|BARCODE=AAAA|SAMPLE=S1 ID> SEQ4|BARCODE=CCCC|SAMPLE=S1 -> SEQ4|BARCODE=CCCC|SAMPLE=S1 ID> SEQ5|BARCODE=CCCC|SAMPLE=S2 -> SEQ5|BARCODE=CCCC|SAMPLE=S1 ID> SEQ6|BARCODE=GGGG|SAMPLE=S2 -> SEQ6|BARCODE=GGGG|SAMPLE=S2 ID> SEQ7|BARCODE=GGGG|SAMPLE=S2 -> SEQ7|BARCODE=GGGG|SAMPLE=S2 <- test_consensusUnify() 0.000 -> test_deletionUnify() ID> SEQ0|BARCODE=AAAA|SAMPLE=S1 -> False ID> SEQ1|BARCODE=AAAA|SAMPLE=S1 -> False ID> SEQ2|BARCODE=AAAA|SAMPLE=S2 -> False ID> SEQ3|BARCODE=AAAA|SAMPLE=S3 -> False ID> SEQ4|BARCODE=CCCC|SAMPLE=S1 -> False ID> SEQ5|BARCODE=CCCC|SAMPLE=S2 -> False ID> SEQ6|BARCODE=GGGG|SAMPLE=S2 -> True ID> SEQ7|BARCODE=GGGG|SAMPLE=S2 -> True <- test_deletionUnify() 0.000 create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py install --root /build/reproducible-path/presto-0.7.2/debian/python3-presto running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_scripts running install_lib creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/UnifyHeaders.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/MaskPrimers.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/EstimateError.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/ConvertHeaders.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/CollapseSeq.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/ClusterSets.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/BuildConsensus.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/AssemblePairs.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/UnifyHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/SplitSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/ParseLog.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/ParseHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/PairSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/MaskPrimers.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/FilterSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/EstimateError.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/ConvertHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/CollapseSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/ClusterSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/BuildConsensus.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/AssemblePairs.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/AlignSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Multiprocessing.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Sequence.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Applications.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Commandline.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/IO.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Annotation.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Defaults.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Version.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Annotation.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Applications.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Commandline.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Defaults.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/IO.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Multiprocessing.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Sequence.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Version.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__init__.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/UnifyHeaders.py to UnifyHeaders.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/SplitSeq.py to SplitSeq.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/ParseLog.py to ParseLog.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/ParseHeaders.py to ParseHeaders.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/PairSeq.py to PairSeq.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/MaskPrimers.py to MaskPrimers.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/FilterSeq.py to FilterSeq.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/EstimateError.py to EstimateError.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/ConvertHeaders.py to ConvertHeaders.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/CollapseSeq.py to CollapseSeq.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/ClusterSets.py to ClusterSets.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/BuildConsensus.py to BuildConsensus.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/AssemblePairs.py to AssemblePairs.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/AlignSets.py to AlignSets.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Annotation.py to Annotation.cpython-313.pyc /usr/lib/python3.13/dist-packages/presto/Annotation.py:293: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.13/dist-packages/presto/Annotation.py:368: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.13/dist-packages/presto/Annotation.py:491: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.13/dist-packages/presto/Annotation.py:493: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.13/dist-packages/presto/Annotation.py:494: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Applications.py to Applications.cpython-313.pyc /usr/lib/python3.13/dist-packages/presto/Applications.py:61: SyntaxWarning: invalid escape sequence '\.' /usr/lib/python3.13/dist-packages/presto/Applications.py:288: SyntaxWarning: invalid escape sequence '\>' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Commandline.py to Commandline.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Defaults.py to Defaults.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/IO.py to IO.cpython-313.pyc /usr/lib/python3.13/dist-packages/presto/IO.py:34: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Multiprocessing.py to Multiprocessing.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Sequence.py to Sequence.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Version.py to Version.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__init__.py to __init__.cpython-313.pyc running install_egg_info running egg_info creating presto.egg-info writing presto.egg-info/PKG-INFO writing dependency_links to presto.egg-info/dependency_links.txt writing requirements to presto.egg-info/requires.txt writing top-level names to presto.egg-info/top_level.txt writing manifest file 'presto.egg-info/SOURCES.txt' reading manifest file 'presto.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'presto.egg-info/SOURCES.txt' Copying presto.egg-info to /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto-0.7.2.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/UnifyHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/SplitSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/ParseLog.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/ParseHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/PairSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/MaskPrimers.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/FilterSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/EstimateError.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/ConvertHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/CollapseSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/ClusterSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/BuildConsensus.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/AssemblePairs.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/AlignSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/UnifyHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/SplitSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ParseLog.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ParseHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/PairSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/MaskPrimers.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/FilterSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/EstimateError.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ConvertHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/CollapseSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ClusterSets.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/BuildConsensus.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/AssemblePairs.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/AlignSets.py to 755 I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/presto-0.7.2/debian/python3-presto running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_scripts running install_lib creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/UnifyHeaders.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/MaskPrimers.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/EstimateError.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/ConvertHeaders.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/CollapseSeq.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/ClusterSets.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/BuildConsensus.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/AssemblePairs.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/UnifyHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/SplitSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/ParseLog.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/ParseHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/PairSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/MaskPrimers.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/FilterSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/EstimateError.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/ConvertHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/CollapseSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/ClusterSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/BuildConsensus.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/AssemblePairs.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/AlignSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Multiprocessing.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Sequence.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Applications.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Commandline.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/IO.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Annotation.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Defaults.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Version.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Applications.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Commandline.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Defaults.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/IO.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Multiprocessing.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Sequence.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Version.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__init__.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/UnifyHeaders.py to UnifyHeaders.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/SplitSeq.py to SplitSeq.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/ParseLog.py to ParseLog.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/ParseHeaders.py to ParseHeaders.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/PairSeq.py to PairSeq.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/MaskPrimers.py to MaskPrimers.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/FilterSeq.py to FilterSeq.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/EstimateError.py to EstimateError.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/ConvertHeaders.py to ConvertHeaders.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/CollapseSeq.py to CollapseSeq.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/ClusterSets.py to ClusterSets.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/BuildConsensus.py to BuildConsensus.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/AssemblePairs.py to AssemblePairs.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/AlignSets.py to AlignSets.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Annotation.py to Annotation.cpython-312.pyc /usr/lib/python3.12/dist-packages/presto/Annotation.py:293: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/presto/Annotation.py:368: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/presto/Annotation.py:491: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/presto/Annotation.py:493: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/presto/Annotation.py:494: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Applications.py to Applications.cpython-312.pyc /usr/lib/python3.12/dist-packages/presto/Applications.py:61: SyntaxWarning: invalid escape sequence '\.' /usr/lib/python3.12/dist-packages/presto/Applications.py:288: SyntaxWarning: invalid escape sequence '\>' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Commandline.py to Commandline.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Defaults.py to Defaults.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/IO.py to IO.cpython-312.pyc /usr/lib/python3.12/dist-packages/presto/IO.py:34: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Multiprocessing.py to Multiprocessing.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Sequence.py to Sequence.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Version.py to Version.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__init__.py to __init__.cpython-312.pyc running install_egg_info running egg_info writing presto.egg-info/PKG-INFO writing dependency_links to presto.egg-info/dependency_links.txt writing requirements to presto.egg-info/requires.txt writing top-level names to presto.egg-info/top_level.txt reading manifest file 'presto.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'presto.egg-info/SOURCES.txt' Copying presto.egg-info to /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto-0.7.2.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.12/UnifyHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/SplitSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/ParseLog.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/ParseHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/PairSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/MaskPrimers.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/FilterSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/EstimateError.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/ConvertHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/CollapseSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/ClusterSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/BuildConsensus.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/AssemblePairs.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/AlignSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/UnifyHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/SplitSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ParseLog.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ParseHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/PairSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/MaskPrimers.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/FilterSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/EstimateError.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ConvertHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/CollapseSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ClusterSets.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/BuildConsensus.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/AssemblePairs.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/AlignSets.py to 755 debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/presto-0.7.2' dh_install mkdir -p debian/presto/usr mv debian/python3-presto/usr/bin debian/presto/usr make[1]: Leaving directory '/build/reproducible-path/presto-0.7.2' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/presto-0.7.2' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/presto-0.7.2' dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-presto' in '../python3-presto_0.7.2-1_arm64.deb'. dpkg-deb: building package 'presto' in '../presto_0.7.2-1_all.deb'. dpkg-genbuildinfo --build=binary -O../presto_0.7.2-1_arm64.buildinfo dpkg-genchanges --build=binary -O../presto_0.7.2-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from presto-0.7.2/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2142681 and its subdirectories I: Current time: Wed Dec 24 12:11:57 -12 2025 I: pbuilder-time-stamp: 1766621517 Thu Dec 25 00:11:57 UTC 2025 I: Signing ./b1/presto_0.7.2-1_arm64.buildinfo as presto_0.7.2-1_arm64.buildinfo.asc Thu Dec 25 00:11:57 UTC 2025 I: Signed ./b1/presto_0.7.2-1_arm64.buildinfo as ./b1/presto_0.7.2-1_arm64.buildinfo.asc Thu Dec 25 00:11:57 UTC 2025 - build #1 for presto/unstable/arm64 on codethink01-arm64 done. Starting cleanup. All cleanup done. Thu Dec 25 00:11:57 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-Iur4BFZ5, removing. /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 17:48 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 17:46 b2 -rw-r--r-- 1 jenkins jenkins 2233 Feb 19 2024 presto_0.7.2-1.dsc -rw------- 1 jenkins jenkins 3336 Nov 21 17:46 rbuildlog.AFlOsFD /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/b1: total 884 -rw-r--r-- 1 jenkins jenkins 157265 Nov 21 17:48 build.log -rw-r--r-- 1 jenkins jenkins 20772 Nov 21 17:48 presto_0.7.2-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2233 Nov 21 17:48 presto_0.7.2-1.dsc -rw-r--r-- 1 jenkins jenkins 239480 Nov 21 17:48 presto_0.7.2-1_all.deb -rw-r--r-- 1 jenkins jenkins 8117 Nov 21 17:48 presto_0.7.2-1_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8999 Nov 21 17:48 presto_0.7.2-1_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2098 Nov 21 17:48 presto_0.7.2-1_arm64.changes -rw-r--r-- 1 jenkins jenkins 2135 Nov 21 17:48 presto_0.7.2-1_source.changes -rw-r--r-- 1 jenkins jenkins 361536 Nov 21 17:48 presto_0.7.2.orig.tar.xz -rw-r--r-- 1 jenkins jenkins 79604 Nov 21 17:48 python3-presto_0.7.2-1_arm64.deb /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/b2: total 0 Thu Nov 21 17:48:58 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Dec 24 12:10:00 -12 2025 I: pbuilder-time-stamp: 1766621400 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 [presto_0.7.2-1.dsc] I: copying [./presto_0.7.2.orig.tar.xz] I: copying [./presto_0.7.2-1.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Feb 19 12:51:18 2024 gpgv: using RSA key 4A31DB5A1EE4096C87399880903649294C33F9B7 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./presto_0.7.2-1.dsc: no acceptable signature found dpkg-source: info: extracting presto in presto-0.7.2 dpkg-source: info: unpacking presto_0.7.2.orig.tar.xz dpkg-source: info: unpacking presto_0.7.2-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2142681/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='c8405f1704b34847bbfdcd5153f53e9f' 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='2142681' 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.aBgKXB6Q/pbuilderrc_HOcn --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.aBgKXB6Q/b1 --logfile b1/build.log presto_0.7.2-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2142681/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: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all, python3-setuptools, python3-biopython, python3-pandas, python3-scipy, python3-packaging, vsearch, cd-hit dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20084 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-packaging; however: Package python3-packaging is not installed. pbuilder-satisfydepends-dummy depends on vsearch; however: Package vsearch is not installed. pbuilder-satisfydepends-dummy depends on cd-hit; however: Package cd-hit 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: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cd-hit{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{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} libxml2{a} libxrender1{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-autocommand{a} python3-biopython{a} python3-cairo{a} python3-chardet{a} python3-dateutil{a} python3-decorator{a} python3-freetype{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pkg-resources{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} vsearch{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra krb5-locales libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-bottleneck python3-bs4 python3-html5lib python3-jinja2 python3-lxml python3-matplotlib python3-numexpr python3-odf python3-olefile python3-openpyxl python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 132 newly installed, 0 to remove and 0 not upgraded. Need to get 91.9 MB of archives. After unpacking 419 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.7-3 [808 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.7-3 [1940 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.7-1 [26.8 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 12 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.7-3 [1902 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.7-1 [9708 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.7-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.0-2 [850 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.0-2 [1838 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 cd-hit arm64 4.8.1-4+b1 [509 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 48 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 62 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.2.0-1 [731 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20241024 [109 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1+b1 [22.5 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 78 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b2 [27.2 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.2-3 [1411 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b2 [25.6 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.0-2+b4 [185 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [1922 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.1-1+b2 [13.8 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libwebpdemux2 arm64 1.4.0-0.1+b1 [110 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.4.0-0.1+b1 [122 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.0-2 [730 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.12.7-1 [1052 B] Get: 115 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [3816 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 python3-pil arm64 10.4.0-1+b1 [498 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 python3-cairo arm64 1.26.1-2+b1 [130 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 121 http://deb.debian.org/debian unstable/main arm64 python3-reportlab all 4.2.5-1 [1117 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 python3-biopython arm64 1.84+dfsg-4+b1 [1644 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 python3-tz all 2024.1-2 [30.9 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-5+b1 [6028 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 python3-scipy arm64 1.13.1-6 [18.2 MB] Get: 132 http://deb.debian.org/debian unstable/main arm64 vsearch arm64 2.29.1-1 [410 kB] Fetched 91.9 MB in 1s (172 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (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 ... 20084 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.7-3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_arm64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:arm64 (3.12.7-3) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20404 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_arm64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_arm64.deb ... 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Unpacking python3-packaging (24.2-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../106-python3-tz_2024.1-2_all.deb ... Unpacking python3-tz (2024.1-2) ... Selecting previously unselected package python3-pandas-lib:arm64. Preparing to unpack .../107-python3-pandas-lib_2.2.3+dfsg-5+b1_arm64.deb ... Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5+b1) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../108-python3-pandas_2.2.3+dfsg-5_all.deb ... Unpacking python3-pandas (2.2.3+dfsg-5) ... Selecting previously unselected package python3-scipy. Preparing to unpack .../109-python3-scipy_1.13.1-6_arm64.deb ... Unpacking python3-scipy (1.13.1-6) ... Selecting previously unselected package vsearch. Preparing to unpack .../110-vsearch_2.29.1-1_arm64.deb ... Unpacking vsearch (2.29.1-1) ... Setting up cd-hit (4.8.1-4+b1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libgraphite2-3:arm64 (1.3.14-2+b1) ... Setting up liblcms2-2:arm64 (2.16-2) ... Setting up libpixman-1-0:arm64 (0.44.0-3) ... Setting up libsharpyuv0:arm64 (1.4.0-0.1+b1) ... Setting up libxau6:arm64 (1:1.0.11-1) ... Setting up libxdmcp6:arm64 (1:1.1.5-1) ... Setting up libkeyutils1:arm64 (1.6.3-4) ... Setting up libxcb1:arm64 (1.17.0-2+b1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-5) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libxcb-render0:arm64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up vsearch (2.29.1-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:arm64 (1.1.0-2+b6) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libdeflate0:arm64 (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ... Setting up libcom-err2:arm64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Dec 25 00:10:27 UTC 2025. Universal Time is now: Thu Dec 25 00:10:27 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... Setting up libfontenc1:arm64 (1:1.1.8-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.82.2-3) ... No schema files found: doing nothing. Setting up libblas3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.15-1) ... Setting up libimagequant0:arm64 (2.18.0-1+b2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-2) ... Setting up autopoint (0.22.5-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libgfortran5:arm64 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:arm64 (1.4.0-0.1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:arm64 (4.5.1+git230720-5) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libopenjp2-7:arm64 (2.5.0-2+b4) ... Setting up python3.13-minimal (3.13.0-2) ... Setting up libx11-6:arm64 (2:1.8.10-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libwebpmux3:arm64 (1.4.0-0.1+b1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b2) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libwebpdemux2:arm64 (1.4.0-0.1+b1) ... Setting up libxext6:arm64 (2:1.3.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libreadline8t64:arm64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:arm64 (10.0.1-1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1+b1) ... Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1+b2) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Setting up python3.13 (3.13.0-2) ... Setting up po-debconf (1.0.21+nmu1) ... 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:arm64 (1.18.2-2) ... Setting up libraqm0:arm64 (0.10.1-1+b2) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up libpython3.12-stdlib:arm64 (3.12.7-3) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libpython3-stdlib:arm64 (3.12.7-1) ... Setting up python3 (3.12.7-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-tz (2024.1-2) ... Setting up python3-pil:arm64 (10.4.0-1+b1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.2-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-cairo (1.26.1-2+b1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-all (3.12.7-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up python3-reportlab (4.2.5-1) ... Setting up dh-python (6.20241024) ... Setting up python3-scipy (1.13.1-6) ... Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5+b1) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.84+dfsg-4+b1) ... 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/presto-0.7.2/ && 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 > ../presto_0.7.2-1_source.changes dpkg-buildpackage: info: source package presto dpkg-buildpackage: info: source version 0.7.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Lance Lin dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 dpkg-source: info: using options from presto-0.7.2/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean running clean removing '/build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it I: pybuild base:311: python3.12 setup.py clean running clean removing '/build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config running config I: pybuild base:311: python3.12 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py build running build running build_py creating /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/__init__.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Version.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Sequence.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Multiprocessing.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/IO.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Defaults.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Commandline.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Applications.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Annotation.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto running build_scripts creating build/scripts-3.13 copying and adjusting bin/AlignSets.py -> build/scripts-3.13 copying and adjusting bin/AssemblePairs.py -> build/scripts-3.13 copying and adjusting bin/BuildConsensus.py -> build/scripts-3.13 copying and adjusting bin/ClusterSets.py -> build/scripts-3.13 copying and adjusting bin/CollapseSeq.py -> build/scripts-3.13 copying and adjusting bin/ConvertHeaders.py -> build/scripts-3.13 copying and adjusting bin/EstimateError.py -> build/scripts-3.13 copying and adjusting bin/FilterSeq.py -> build/scripts-3.13 copying and adjusting bin/MaskPrimers.py -> build/scripts-3.13 copying and adjusting bin/PairSeq.py -> build/scripts-3.13 copying and adjusting bin/ParseHeaders.py -> build/scripts-3.13 copying and adjusting bin/ParseLog.py -> build/scripts-3.13 copying and adjusting bin/SplitSeq.py -> build/scripts-3.13 copying and adjusting bin/UnifyHeaders.py -> build/scripts-3.13 changing mode of build/scripts-3.13/AlignSets.py from 644 to 755 changing mode of build/scripts-3.13/AssemblePairs.py from 644 to 755 changing mode of build/scripts-3.13/BuildConsensus.py from 644 to 755 changing mode of build/scripts-3.13/ClusterSets.py from 644 to 755 changing mode of build/scripts-3.13/CollapseSeq.py from 644 to 755 changing mode of build/scripts-3.13/ConvertHeaders.py from 644 to 755 changing mode of build/scripts-3.13/EstimateError.py from 644 to 755 changing mode of build/scripts-3.13/FilterSeq.py from 644 to 755 changing mode of build/scripts-3.13/MaskPrimers.py from 644 to 755 changing mode of build/scripts-3.13/PairSeq.py from 644 to 755 changing mode of build/scripts-3.13/ParseHeaders.py from 644 to 755 changing mode of build/scripts-3.13/ParseLog.py from 644 to 755 changing mode of build/scripts-3.13/SplitSeq.py from 644 to 755 changing mode of build/scripts-3.13/UnifyHeaders.py from 644 to 755 I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/__init__.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Version.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Sequence.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Multiprocessing.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/IO.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Defaults.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Commandline.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Applications.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Annotation.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto running build_scripts creating build/scripts-3.12 copying and adjusting bin/AlignSets.py -> build/scripts-3.12 copying and adjusting bin/AssemblePairs.py -> build/scripts-3.12 copying and adjusting bin/BuildConsensus.py -> build/scripts-3.12 copying and adjusting bin/ClusterSets.py -> build/scripts-3.12 copying and adjusting bin/CollapseSeq.py -> build/scripts-3.12 copying and adjusting bin/ConvertHeaders.py -> build/scripts-3.12 copying and adjusting bin/EstimateError.py -> build/scripts-3.12 copying and adjusting bin/FilterSeq.py -> build/scripts-3.12 copying and adjusting bin/MaskPrimers.py -> build/scripts-3.12 copying and adjusting bin/PairSeq.py -> build/scripts-3.12 copying and adjusting bin/ParseHeaders.py -> build/scripts-3.12 copying and adjusting bin/ParseLog.py -> build/scripts-3.12 copying and adjusting bin/SplitSeq.py -> build/scripts-3.12 copying and adjusting bin/UnifyHeaders.py -> build/scripts-3.12 changing mode of build/scripts-3.12/AlignSets.py from 644 to 755 changing mode of build/scripts-3.12/AssemblePairs.py from 644 to 755 changing mode of build/scripts-3.12/BuildConsensus.py from 644 to 755 changing mode of build/scripts-3.12/ClusterSets.py from 644 to 755 changing mode of build/scripts-3.12/CollapseSeq.py from 644 to 755 changing mode of build/scripts-3.12/ConvertHeaders.py from 644 to 755 changing mode of build/scripts-3.12/EstimateError.py from 644 to 755 changing mode of build/scripts-3.12/FilterSeq.py from 644 to 755 changing mode of build/scripts-3.12/MaskPrimers.py from 644 to 755 changing mode of build/scripts-3.12/PairSeq.py from 644 to 755 changing mode of build/scripts-3.12/ParseHeaders.py from 644 to 755 changing mode of build/scripts-3.12/ParseLog.py from 644 to 755 changing mode of build/scripts-3.12/SplitSeq.py from 644 to 755 changing mode of build/scripts-3.12/UnifyHeaders.py from 644 to 755 dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: cp -r /build/reproducible-path/presto-0.7.2/bin /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build; I: pybuild base:311: cd /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build; python3.13 -m unittest discover -v /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Annotation.py:293: SyntaxWarning: invalid escape sequence '\s' sub_regex = '[%s\s]+' % re.escape(''.join(delimiter)) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Annotation.py:368: SyntaxWarning: invalid escape sequence '\s' sub_regex = '[%s\s]+' % re.escape(''.join(delimiter[1:])) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Annotation.py:491: SyntaxWarning: invalid escape sequence '\s' header['SPECIES'] = re.sub('\s', '_', fields[2]) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Annotation.py:493: SyntaxWarning: invalid escape sequence '\(' header['FUNCTIONALITY'] = re.sub('[\(\)\[\]]', '', fields[3]) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Annotation.py:494: SyntaxWarning: invalid escape sequence '\s' header['PARTIAL'] = 'FALSE' if re.sub('\s', '', fields[13]) == '' else 'TRUE' /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/IO.py:34: SyntaxWarning: invalid escape sequence '\s' if replace_special: parse_id = lambda x: re.sub('[\s,=|]+', '_', x) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Applications.py:61: SyntaxWarning: invalid escape sequence '\.' version = re.sub('\.linux.*$','',version) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Applications.py:288: SyntaxWarning: invalid escape sequence '\>' id_regex = re.compile('([0-9]+\t[0-9]+nt, \>)(.+)(\.\.\.)') test_collapseAnnotation (tests.test_Annotation.TestAnnotation.test_collapseAnnotation) ... ok test_getCoordKey (tests.test_Annotation.TestAnnotation.test_getCoordKey) ... ok test_mergeAnnotation (tests.test_Annotation.TestAnnotation.test_mergeAnnotation) ... ok test_renameAnnotation (tests.test_Annotation.TestAnnotation.test_renameAnnotation) ... ok test_alignAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_alignAssembly) ... skipped '-> alignAssembly() skipped\n' test_makeBlastnDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeBlastnDb) ... skipped '-> makeBlastnDb() skipped\n' test_makeUSearchDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeUSearchDb) ... skipped '-> makeUSearchDb() skipped\n' test_referenceAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_referenceAssembly) ... skipped '-> referenceAssembly() skipped\n' test_runBlastn (tests.test_AssemblePairs.TestAssemblePairs.test_runBlastn) ... skipped '-> runBlastn() skipped\n' test_runUSearch (tests.test_AssemblePairs.TestAssemblePairs.test_runUSearch) ... skipped '-> runUSearch() skipped\n' test_calculateSetError (tests.test_BuildConsensus.TestBuildConsensus.test_calculateSetError) ... ok test_deleteSeqPositions (tests.test_BuildConsensus.TestBuildConsensus.test_deleteSeqPositions) ... ok test_findGapPositions (tests.test_BuildConsensus.TestBuildConsensus.test_findGapPositions) ... ok test_frequencyConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_frequencyConsensus) ... ok test_qualityConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_qualityConsensus) ... ok test_runCDHit (tests.test_ClusterSets.TestClusterSets.test_runCDHit) ... ok test_runUClust (tests.test_ClusterSets.TestClusterSets.test_runUClust) ... ok test_checkSeqEqual (tests.test_CollapseSeq.TestCollapseSeq.test_checkSeqEqual) ... ok test_convert454Header (tests.test_ConvertHeaders.TestConvertHeaders.test_convert454Header) ... ok test_convertGenbankHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertGenbankHeader) ... ok test_convertGenericHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertGenericHeader) ... ok test_convertIMGTHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertIMGTHeader) ... ok test_convertIlluminaHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertIlluminaHeader) ... ok test_convertSRAHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertSRAHeader) ... ok test_calculateDistances (tests.test_EstimateError.TestEstimateError.test_calculateDistances) ... /usr/lib/python3/dist-packages/Bio/SeqRecord.py:228: BiopythonDeprecationWarning: Using a string as the sequence is deprecated and will raise a TypeError in future. It has been converted to a Seq object. warnings.warn( ok test_countMismatches (tests.test_EstimateError.TestEstimateError.test_countMismatches) ... ok test_initializeMismatchDictionary (tests.test_EstimateError.TestEstimateError.test_initializeMismatchDictionary) ... ok test_getFileType (tests.test_IO.TestIO.test_getFileType) ... ok test_extractAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_extractAlignment) ... ok test_localAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_localAlignment) ... -> test_collapseAnnotation() OrderedDict({'ID': 'SEQ1', 'TEST1': 'A', 'TEST2': 1, 'TEST3': 'First'}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'B', 'TEST2': 2, 'TEST3': 'Second'}) OrderedDict({'ID': 'SEQ1', 'TEST1': ['A', 'B'], 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'AB', 'TEST2': '12', 'TEST3': 'FirstSecond'}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '1', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '2', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '3', 'TEST3': ['First', 'Second']}) <- test_collapseAnnotation() 0.000 -> test_getCoordKey() ['MISEQ:132:000000000-A2F3U:1:1101:14340:1555', 'HWI-EAS209_0006_FC706VJ:5:58:5894:21141', 'MS6_33112:1:1101:18371:1066'] ['SRR001666.1', 'SRR735691.1', 'SRR1383326.1', 'SRR1383326.1', 'ERR346596.6'] ['000034_0199_0169', 'GXGJ56Z01AE06X'] <- test_getCoordKey() 0.000 -> test_mergeAnnotation() OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,C,C', 'TEST2': '1,2,3', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'C,C,A,B', 'TEST2': '3,1,2', 'TEST3': ['First', 'Second']}) <- test_mergeAnnotation() 0.000 -> test_renameAnnotation() OrderedDict({'ID': 'SEQ1', 'RENAMED1': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'RENAMED2': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2,First,Second'}) <- test_renameAnnotation() 0.000 -> test_calculateSetError() Frequency consensus error> REF> CGGCGTAA SEQ1> CGGCGTAA SEQ2> CCNNGTAA SEQ3> CGGC--TA SEQ4> CGNN--TA SEQ5> CGGC--AA ERROR> 0.250000 Quality consensus error> REF> CGGCNNAA SEQ1> CGGCGTAA SEQ2> CCNNGTAA SEQ3> CGGC--TA SEQ4> CGNN--TA SEQ5> CGGC--AA ERROR> 0.233333 <- test_calculateSetError() 0.000 -> test_deleteSeqPositions() MAX_GAP=0.4> CGGCAA MAX_GAP=0.8> CGGCGTAA <- test_deleteSeqPositions() 0.000 -> test_findGapPositions() MAX_GAP=0.4> [4, 5] MAX_GAP=0.8> [] <- test_findGapPositions() 0.000 -> test_frequencyConsensus() MIN_FREQ=0.2> CGGCGTAA MIN_FREQ=0.8> CGGCGTNA <- test_frequencyConsensus() 0.000 -> test_qualityConsensus() MIN_QUAL=0> CGGCGTAA [90, 90, 36, 36, 16, 16, 72, 90] MIN_QUAL=20> CGGCNNAA [90, 90, 36, 36, 0, 0, 72, 90] MIN_FREQ=0.8> CGGCNNNA [90, 90, 36, 36, 0, 0, 0, 90] <- test_qualityConsensus() 0.000 -> test_runCDHit() FULL_LENGTH> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} TRIMMED> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} ZERO_LENGTH> None <- test_runCDHit() 0.029 -> test_runUClust() FULL_LENGTH> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} TRIMMED> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} ZERO_LENGTH> None <- test_runUClust() 0.025 -> test_checkSeqEqual() DNA Equality> SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA EQUAL> True SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA SEQ3|COUNT=3> CCACGTTTTACTAATTAATA EQUAL> False SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA SEQ4|COUNT=4> CCACGTTTTANTAATTAATA EQUAL> True SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA SEQ3|COUNT=3> CCACGTTTTACTAATTAATA EQUAL> False SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA SEQ4|COUNT=4> CCACGTTTTANTAATTAATA EQUAL> True SEQ3|COUNT=3> CCACGTTTTACTAATTAATA SEQ4|COUNT=4> CCACGTTTTANTAATTAATA EQUAL> True <- test_checkSeqEqual() 0.000 -> test_convert454Header() OrderedDict({'ID': '000034_0199_0169', 'LENGTH': '437', 'UACCNO': 'GNDG01201ARRCR'}) OrderedDict({'ID': 'GXGJ56Z01AE06X', 'LENGTH': '222'}) <- test_convert454Header() 0.000 -> test_convertGenbankHeader() OrderedDict({'ID': 'CM000663.2', 'GI': '568336023', 'SOURCE': 'gb', 'DESC': 'Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) OrderedDict({'ID': 'CM000663.2', 'DESC': 'Homo_sapiens_chromosome_1__GRCh38_reference_primary_assembly'}) <- test_convertGenbankHeader() 0.000 -> test_convertGenericHeader() OrderedDict({'ID': 'gi_568336023_gb_CM000663.2_Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) OrderedDict({'ID': 'CM000663.2_Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) OrderedDict({'ID': 'M99641_IGHV1-18*01_Homo_sapiens_F_V-REGION_188..483_296_nt_1_296+24_320_'}) OrderedDict({'ID': "Z29978_IGHV1-69*07_Homo_sapiens_F_V-REGION_1..233_233_nt_1_233+58_291_partial_in_5'_and_in_3'_"}) OrderedDict({'ID': 'AB019439_IGHV(III)-22-2*01_Homo_sapiens_P_L-PART1+V-EXON_168065..168119+168222..168262_96_nt_1_96+0_96_'}) OrderedDict({'ID': 'AE000659_TRAV11*01_Homo_sapiens_(P)_V-REGION_85121..85397_276_nt_1_276+42_318_'}) <- test_convertGenericHeader() 0.000 -> test_convertIMGTHeader() OrderedDict({'ID': 'IGHV1-18*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'F', 'PARTIAL': 'FALSE', 'ACCESSION': 'M99641'}) OrderedDict({'ID': 'IGHV1-69*07', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'F', 'PARTIAL': 'TRUE', 'ACCESSION': 'Z29978'}) OrderedDict({'ID': 'IGHV(III)-22-2*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'L-PART1+V-EXON', 'FUNCTIONALITY': 'P', 'PARTIAL': 'FALSE', 'ACCESSION': 'AB019439'}) OrderedDict({'ID': 'TRAV11*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'P', 'PARTIAL': 'FALSE', 'ACCESSION': 'AE000659'}) OrderedDict({'ID': 'IGHV1-18*01'}) OrderedDict({'ID': 'IGHV1-69*07'}) OrderedDict({'ID': 'IGHV(III)-22-2*01'}) OrderedDict({'ID': 'TRAV11*01'}) <- test_convertIMGTHeader() 0.000 -> test_convertIlluminaHeader() OrderedDict({'ID': 'MISEQ:132:000000000-A2F3U:1:1101:14340:1555', 'INDEX': 'ATCACG', 'READ': '1'}) OrderedDict({'ID': 'HWI-EAS209_0006_FC706VJ:5:58:5894:21141', 'INDEX': 'ATCACG', 'READ': '1'}) OrderedDict({'ID': 'MS6_33112:1:1101:18371:1066', 'READ': '1'}) <- test_convertIlluminaHeader() 0.000 -> test_convertSRAHeader() OrderedDict({'ID': 'SRR001666.1', 'DESC': '071112_SLXA-EAS1_s_7:5:1:817:345', 'LENGTH': '36'}) OrderedDict({'ID': 'SRR735691.1', 'DESC': 'GXGJ56Z01AE06X', 'LENGTH': '222'}) OrderedDict({'ID': 'SRR1383326.1', 'DESC': '1', 'LENGTH': '250'}) OrderedDict({'ID': 'SRR1383326.1', 'READ': '2', 'DESC': '1', 'LENGTH': '250'}) OrderedDict({'ID': 'ERR346596.6', 'DESC': 'BS-DSFCONTROL04:4:000000000-A3F0Y:1:1101:13220:1649/1'}) <- test_convertSRAHeader() 0.000 -> test_calculateDistances() <- test_calculateDistances() 0.002 -> test_countMismatches() <- test_countMismatches() 0.001 -> test_initializeMismatchDictionary() <- test_initializeMismatchDictionary() 0.000 -> test_getFileType() <- test_getFileType() 0.000 -> test_extractAlignment() SEQ1> SEQ> CCACGTTTTAGTAATTAATA ALN-SEQ> CCACGTTTTAGT ALN-PR> ----GTTTTAGT PRIMER> GTTTTAGT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ2> SEQ> CCNCGTTTTAGTAATTAATA ALN-SEQ> CCNCGTTTTAGT ALN-PR> ----GTTTTAGT PRIMER> GTTTTAGT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ3> SEQ> GGGCGTTTTAGTAATTAATA ALN-SEQ> GGGCGTTTTAGT ALN-PR> ----GTTTTAGT PRIMER> GTTTTAGT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTTACT ALN-PR> ----GTTTTACT PRIMER> GTTTTACT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNNACT ALN-PR> ----NNNNNACT PRIMER> NNNNNACT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNNACT ALN-PR> ----TANNNACT PRIMER> TANNNACT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> NNNNNNNNNNNN ALN-PR> ----NNNNNNNN PRIMER> NNNNNNNN START> 4 END> 12 GAPS> 0 ERROR> 0.000000 <- test_extractAlignment() 0.000 -> test_localAlignment() TEST Ns> SEQ1> SEQ> CCACGTTTTAGTAATTAATA ALN-SEQ> CCACGTTTTAGTAATTAATA ALN-PR> -CACGTTTT----------- PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ2> SEQ> CCNCGTTTTAGTAATTAATA ALN-SEQ> CCNCGTTTTAGTAATTAATA ALN-PR> -CACGTTTT----------- PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.125000 ok test_maskSeq (tests.test_MaskPrimers.TestMaskPrimers.test_maskSeq) ... ok test_scoreAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_scoreAlignment) ... ok test_calculateSetError (tests.test_Sequence.TestSequence.test_calculateSetError) ... ok test_filterQuality (tests.test_Sequence.TestSequence.test_filterQuality) ... ok test_meanQuality (tests.test_Sequence.TestSequence.test_meanQuality) ... ok test_scoreDNA (tests.test_Sequence.TestSequence.test_scoreDNA) ... ok test_scoreSeqPair (tests.test_Sequence.TestSequence.test_scoreSeqPair) ... SEQ3> SEQ> GGGCGTTTTAGTAATTAATA ALN-SEQ> GGGCGTTTTAGTAATTAATA ALN-PR> -GGCGTTTT----------- PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTTACTAATTAATA ALN-PR> GGC-GTTTT----------- PRIMER> PR2 START> 0 END> 9 GAPS> 1 ERROR> 0.250000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNNACTAATTAATA ALN-PR> ------------ANATAA-- PRIMER> PR3 START> 12 END> 18 GAPS> 0 ERROR> 0.375000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNNACTAATTAATA ALN-PR> -GGANA-------------- PRIMER> PR3 START> 1 END> 6 GAPS> 0 ERROR> 0.375000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> None ALN-PR> None PRIMER> None START> None END> None GAPS> 0 ERROR> 1.000000 TEST INDELS> SEQ1> SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG ALN-SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG ALN-PR> ---------------ATACGTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 15 END> 38 GAPS> 0 ERROR> 0.083333 SEQ2> SEQ> CGGATCTTCTACTCAAAACCGTCCTCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG ALN-SEQ> CGGATCTTCTACTCAAAACCGTCC-TCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG ALN-PR> --------------AATAC-GTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 14 END> 38 GAPS> 2 ERROR> 0.208333 SEQ3> SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTGATCTGTTTTACATGGGGGCATCACCCAG ALN-SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTG-ATCTGTTTTACATGGGGGCATCACCCAG ALN-PR> ---------------AATACGTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 15 END> 38 GAPS> 1 ERROR> 0.125000 SEQ4> SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT ALN-SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT ALN-PR> ------CATCT-TCCTCTA------------------------------------------- PRIMER> PR2 START> 6 END> 19 GAPS> 1 ERROR> 0.250000 SEQ5> SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG ALN-SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG ALN-PR> ------CATCTTCCTCTA-------------------------------------------- PRIMER> PR2 START> 6 END> 18 GAPS> 0 ERROR> 0.166667 SEQ6> SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA ALN-SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA ALN-PR> TCT-TCCTCTA--------------------------------------------------- PRIMER> PR2 START> 0 END> 11 GAPS> 1 ERROR> 0.250000 SEQ7> SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> --GTGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 2 END> 15 GAPS> 1 ERROR> 0.083333 SEQ8> SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 3 END> 15 GAPS> 1 ERROR> 0.166667 SEQ9> SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 3 END> 15 GAPS> 1 ERROR> 0.333333 SEQ10> SEQ> -------------------------------------------------------------- ALN-SEQ> None ALN-PR> None PRIMER> None START> None END> None GAPS> 0 ERROR> 1.000000 <- test_localAlignment() 0.028 -> test_maskSeq() TEST CUT> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> AGTAATTAATA TEST MASK> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> NNNNNNAGTAATTAATA TEST TRIM> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> CGTTTTAGTAATTAATA TEST TAG> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> CCACGTTTTAGTAATTAATA <- test_maskSeq() 0.001 -> test_scoreAlignment() SEQ1> SEQ> CCACGTTTTAGTAATTAATA ALN-SEQ> CCACGTTTT ALN-PR> -CACGTTTT PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ2> SEQ> CCNCGTTTTAGTAATTAATA ALN-SEQ> CCNCGTTTT ALN-PR> -CACGTTTT PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.125000 SEQ3> SEQ> GGGCGTTTTAGTAATTAATA ALN-SEQ> GGGCGTTTT ALN-PR> -GGCGTTTT PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTT ALN-PR> -GGCGTTTT PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.250000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNN ALN-PR> -GGCGTTTT PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.750000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNN ALN-PR> -GGANATAA PRIMER> PR3 START> 1 END> 9 GAPS> 0 ERROR> 0.375000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> NNNNNNNNN ALN-PR> -CACGTTTT PRIMER> None START> 1 END> 9 GAPS> 0 ERROR> 1.000000 <- test_scoreAlignment() 0.007 -> test_calculateSetError() REF> CGGCGTAA 0.4347826086956522 REF> NNNNNNNN 1.0 <- test_calculateSetError() 0.000 -> test_filterQuality() RESULT> True 25 RESULT> False 5 RESULT> False 0 <- test_filterQuality() 0.000 -> test_meanQuality() RESULT> 25 [30, 30, 20, 20, 30, 30, 40, 40] RESULT> 5 [30, 30, 0, 0, 30, 30, 20, 20] RESULT> 0 [0, 0, 0, 0, 0, 0, 0, 0] <- test_meanQuality() 0.000 -> test_scoreDNA() Default DNA Scores> A==A> 1 A==T> 0 A==R> 1 U==T> 1 A==N> 1 N==A> 1 A==-> 0 -==A> 0 Symmetric DNA Scores> A==A> 1 A==T> 0 A==R> 1 U==T> 1 A==N> 1 N==A> 1 A==-> 1 -==A> 1 Asymmetric DNA Scores> A==A> 1 A==T> 0 A==R> 1 U==T> 1 A==N> 1 N==A> 0 A==-> 1 -==A> 0 <- test_scoreDNA() 0.000 -> test_scoreSeqPair() Default DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ6> NNNNNNAA SEQ7> --------ok test_weightDNA (tests.test_Sequence.TestSequence.test_weightDNA) ... ok test_consensusUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_consensusUnify) ... ok test_deletionUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_deletionUnify) ... ok ---------------------------------------------------------------------- Ran 40 tests in 0.110s OK (skipped=6) SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ7> -------- SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 Asymmetric DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 3 WEIGHT> 8 ERROR> 0.625000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ7> -------- SEQ8> CG------ SCORE> 0 WEIGHT> 8 ERROR> 1.000000 Masked DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 5 WEIGHT> 6 ERROR> 0.166667 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 3 WEIGHT> 6 ERROR> 0.500000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 2 WEIGHT> 2 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 3 WEIGHT> 6 ERROR> 0.500000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 4 WEIGHT> 6 ERROR> 0.333333 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 1 WEIGHT> 2 ERROR> 0.500000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 0 WEIGHT> 6 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 2 WEIGHT> 6 ERROR> 0.666667 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 6 ERROR> 0.166667 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 2 WEIGHT> 2 ERROR> 0.000000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 1 WEIGHT> 2 ERROR> 0.500000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 2 WEIGHT> 6 ERROR> 0.666667 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 6 ERROR> 0.333333 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ7> -------- SCORE> 0 WEIGHT> 2 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 0 WEIGHT> 2 ERROR> 1.000000 SEQ7> -------- SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 <- test_scoreSeqPair() 0.006 -> test_weightDNA() DNA Weight> SEQ1> 8 SEQ2> 6 SEQ3> 8 SEQ4> 6 SEQ5> 0 SEQ6> 2 SEQ7> 8 SEQ8> 8 AA Weight> SEQ1> 8 SEQ2> 6 SEQ3> 8 SEQ4> 6 <- test_weightDNA() 0.000 -> test_consensusUnify() ID> SEQ0|BARCODE=AAAA|SAMPLE=S1 -> SEQ0|BARCODE=AAAA|SAMPLE=S1 ID> SEQ1|BARCODE=AAAA|SAMPLE=S1 -> SEQ1|BARCODE=AAAA|SAMPLE=S1 ID> SEQ2|BARCODE=AAAA|SAMPLE=S2 -> SEQ2|BARCODE=AAAA|SAMPLE=S1 ID> SEQ3|BARCODE=AAAA|SAMPLE=S3 -> SEQ3|BARCODE=AAAA|SAMPLE=S1 ID> SEQ4|BARCODE=CCCC|SAMPLE=S1 -> SEQ4|BARCODE=CCCC|SAMPLE=S1 ID> SEQ5|BARCODE=CCCC|SAMPLE=S2 -> SEQ5|BARCODE=CCCC|SAMPLE=S1 ID> SEQ6|BARCODE=GGGG|SAMPLE=S2 -> SEQ6|BARCODE=GGGG|SAMPLE=S2 ID> SEQ7|BARCODE=GGGG|SAMPLE=S2 -> SEQ7|BARCODE=GGGG|SAMPLE=S2 <- test_consensusUnify() 0.000 -> test_deletionUnify() ID> SEQ0|BARCODE=AAAA|SAMPLE=S1 -> False ID> SEQ1|BARCODE=AAAA|SAMPLE=S1 -> False ID> SEQ2|BARCODE=AAAA|SAMPLE=S2 -> False ID> SEQ3|BARCODE=AAAA|SAMPLE=S3 -> False ID> SEQ4|BARCODE=CCCC|SAMPLE=S1 -> False ID> SEQ5|BARCODE=CCCC|SAMPLE=S2 -> False ID> SEQ6|BARCODE=GGGG|SAMPLE=S2 -> True ID> SEQ7|BARCODE=GGGG|SAMPLE=S2 -> True <- test_deletionUnify() 0.000 I: pybuild pybuild:308: cp -r /build/reproducible-path/presto-0.7.2/bin /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build; I: pybuild base:311: cd /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build; python3.12 -m unittest discover -v /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:293: SyntaxWarning: invalid escape sequence '\s' sub_regex = '[%s\s]+' % re.escape(''.join(delimiter)) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:368: SyntaxWarning: invalid escape sequence '\s' sub_regex = '[%s\s]+' % re.escape(''.join(delimiter[1:])) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:491: SyntaxWarning: invalid escape sequence '\s' header['SPECIES'] = re.sub('\s', '_', fields[2]) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:493: SyntaxWarning: invalid escape sequence '\(' header['FUNCTIONALITY'] = re.sub('[\(\)\[\]]', '', fields[3]) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:494: SyntaxWarning: invalid escape sequence '\s' header['PARTIAL'] = 'FALSE' if re.sub('\s', '', fields[13]) == '' else 'TRUE' /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/IO.py:34: SyntaxWarning: invalid escape sequence '\s' if replace_special: parse_id = lambda x: re.sub('[\s,=|]+', '_', x) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Applications.py:61: SyntaxWarning: invalid escape sequence '\.' version = re.sub('\.linux.*$','',version) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Applications.py:288: SyntaxWarning: invalid escape sequence '\>' id_regex = re.compile('([0-9]+\t[0-9]+nt, \>)(.+)(\.\.\.)') test_collapseAnnotation (tests.test_Annotation.TestAnnotation.test_collapseAnnotation) ... ok test_getCoordKey (tests.test_Annotation.TestAnnotation.test_getCoordKey) ... ok test_mergeAnnotation (tests.test_Annotation.TestAnnotation.test_mergeAnnotation) ... ok test_renameAnnotation (tests.test_Annotation.TestAnnotation.test_renameAnnotation) ... ok test_alignAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_alignAssembly) ... skipped '-> alignAssembly() skipped\n' test_makeBlastnDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeBlastnDb) ... skipped '-> makeBlastnDb() skipped\n' test_makeUSearchDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeUSearchDb) ... skipped '-> makeUSearchDb() skipped\n' test_referenceAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_referenceAssembly) ... skipped '-> referenceAssembly() skipped\n' test_runBlastn (tests.test_AssemblePairs.TestAssemblePairs.test_runBlastn) ... skipped '-> runBlastn() skipped\n' test_runUSearch (tests.test_AssemblePairs.TestAssemblePairs.test_runUSearch) ... skipped '-> runUSearch() skipped\n' test_calculateSetError (tests.test_BuildConsensus.TestBuildConsensus.test_calculateSetError) ... ok test_deleteSeqPositions (tests.test_BuildConsensus.TestBuildConsensus.test_deleteSeqPositions) ... ok test_findGapPositions (tests.test_BuildConsensus.TestBuildConsensus.test_findGapPositions) ... ok test_frequencyConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_frequencyConsensus) ... ok test_qualityConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_qualityConsensus) ... ok test_runCDHit (tests.test_ClusterSets.TestClusterSets.test_runCDHit) ... ok test_runUClust (tests.test_ClusterSets.TestClusterSets.test_runUClust) ... ok test_checkSeqEqual (tests.test_CollapseSeq.TestCollapseSeq.test_checkSeqEqual) ... ok test_convert454Header (tests.test_ConvertHeaders.TestConvertHeaders.test_convert454Header) ... ok test_convertGenbankHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertGenbankHeader) ... ok test_convertGenericHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertGenericHeader) ... ok test_convertIMGTHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertIMGTHeader) ... ok test_convertIlluminaHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertIlluminaHeader) ... ok test_convertSRAHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertSRAHeader) ... ok test_calculateDistances (tests.test_EstimateError.TestEstimateError.test_calculateDistances) ... /usr/lib/python3/dist-packages/Bio/SeqRecord.py:228: BiopythonDeprecationWarning: Using a string as the sequence is deprecated and will raise a TypeError in future. It has been converted to a Seq object. warnings.warn( ok test_countMismatches (tests.test_EstimateError.TestEstimateError.test_countMismatches) ... ok test_initializeMismatchDictionary (tests.test_EstimateError.TestEstimateError.test_initializeMismatchDictionary) ... ok test_getFileType (tests.test_IO.TestIO.test_getFileType) ... ok test_extractAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_extractAlignment) ... ok test_localAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_localAlignment) ... -> test_collapseAnnotation() OrderedDict({'ID': 'SEQ1', 'TEST1': 'A', 'TEST2': 1, 'TEST3': 'First'}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'B', 'TEST2': 2, 'TEST3': 'Second'}) OrderedDict({'ID': 'SEQ1', 'TEST1': ['A', 'B'], 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'AB', 'TEST2': '12', 'TEST3': 'FirstSecond'}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '1', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '2', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '3', 'TEST3': ['First', 'Second']}) <- test_collapseAnnotation() 0.000 -> test_getCoordKey() ['MISEQ:132:000000000-A2F3U:1:1101:14340:1555', 'HWI-EAS209_0006_FC706VJ:5:58:5894:21141', 'MS6_33112:1:1101:18371:1066'] ['SRR001666.1', 'SRR735691.1', 'SRR1383326.1', 'SRR1383326.1', 'ERR346596.6'] ['000034_0199_0169', 'GXGJ56Z01AE06X'] <- test_getCoordKey() 0.000 -> test_mergeAnnotation() OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,C,C', 'TEST2': '1,2,3', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'C,C,A,B', 'TEST2': '3,1,2', 'TEST3': ['First', 'Second']}) <- test_mergeAnnotation() 0.000 -> test_renameAnnotation() OrderedDict({'ID': 'SEQ1', 'RENAMED1': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'RENAMED2': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2,First,Second'}) <- test_renameAnnotation() 0.000 -> test_calculateSetError() Frequency consensus error> REF> CGGCGTAA SEQ1> CGGCGTAA SEQ2> CCNNGTAA SEQ3> CGGC--TA SEQ4> CGNN--TA SEQ5> CGGC--AA ERROR> 0.250000 Quality consensus error> REF> CGGCNNAA SEQ1> CGGCGTAA SEQ2> CCNNGTAA SEQ3> CGGC--TA SEQ4> CGNN--TA SEQ5> CGGC--AA ERROR> 0.233333 <- test_calculateSetError() 0.000 -> test_deleteSeqPositions() MAX_GAP=0.4> CGGCAA MAX_GAP=0.8> CGGCGTAA <- test_deleteSeqPositions() 0.000 -> test_findGapPositions() MAX_GAP=0.4> [4, 5] MAX_GAP=0.8> [] <- test_findGapPositions() 0.000 -> test_frequencyConsensus() MIN_FREQ=0.2> CGGCGTAA MIN_FREQ=0.8> CGGCGTNA <- test_frequencyConsensus() 0.000 -> test_qualityConsensus() MIN_QUAL=0> CGGCGTAA [90, 90, 36, 36, 16, 16, 72, 90] MIN_QUAL=20> CGGCNNAA [90, 90, 36, 36, 0, 0, 72, 90] MIN_FREQ=0.8> CGGCNNNA [90, 90, 36, 36, 0, 0, 0, 90] <- test_qualityConsensus() 0.000 -> test_runCDHit() FULL_LENGTH> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} TRIMMED> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} ZERO_LENGTH> None <- test_runCDHit() 0.016 -> test_runUClust() FULL_LENGTH> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} TRIMMED> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} ZERO_LENGTH> None <- test_runUClust() 0.027 -> test_checkSeqEqual() DNA Equality> SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA EQUAL> True SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA SEQ3|COUNT=3> CCACGTTTTACTAATTAATA EQUAL> False SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA SEQ4|COUNT=4> CCACGTTTTANTAATTAATA EQUAL> True SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA SEQ3|COUNT=3> CCACGTTTTACTAATTAATA EQUAL> False SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA SEQ4|COUNT=4> CCACGTTTTANTAATTAATA EQUAL> True SEQ3|COUNT=3> CCACGTTTTACTAATTAATA SEQ4|COUNT=4> CCACGTTTTANTAATTAATA EQUAL> True <- test_checkSeqEqual() 0.000 -> test_convert454Header() OrderedDict({'ID': '000034_0199_0169', 'LENGTH': '437', 'UACCNO': 'GNDG01201ARRCR'}) OrderedDict({'ID': 'GXGJ56Z01AE06X', 'LENGTH': '222'}) <- test_convert454Header() 0.000 -> test_convertGenbankHeader() OrderedDict({'ID': 'CM000663.2', 'GI': '568336023', 'SOURCE': 'gb', 'DESC': 'Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) OrderedDict({'ID': 'CM000663.2', 'DESC': 'Homo_sapiens_chromosome_1__GRCh38_reference_primary_assembly'}) <- test_convertGenbankHeader() 0.000 -> test_convertGenericHeader() OrderedDict({'ID': 'gi_568336023_gb_CM000663.2_Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) OrderedDict({'ID': 'CM000663.2_Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) OrderedDict({'ID': 'M99641_IGHV1-18*01_Homo_sapiens_F_V-REGION_188..483_296_nt_1_296+24_320_'}) OrderedDict({'ID': "Z29978_IGHV1-69*07_Homo_sapiens_F_V-REGION_1..233_233_nt_1_233+58_291_partial_in_5'_and_in_3'_"}) OrderedDict({'ID': 'AB019439_IGHV(III)-22-2*01_Homo_sapiens_P_L-PART1+V-EXON_168065..168119+168222..168262_96_nt_1_96+0_96_'}) OrderedDict({'ID': 'AE000659_TRAV11*01_Homo_sapiens_(P)_V-REGION_85121..85397_276_nt_1_276+42_318_'}) <- test_convertGenericHeader() 0.000 -> test_convertIMGTHeader() OrderedDict({'ID': 'IGHV1-18*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'F', 'PARTIAL': 'FALSE', 'ACCESSION': 'M99641'}) OrderedDict({'ID': 'IGHV1-69*07', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'F', 'PARTIAL': 'TRUE', 'ACCESSION': 'Z29978'}) OrderedDict({'ID': 'IGHV(III)-22-2*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'L-PART1+V-EXON', 'FUNCTIONALITY': 'P', 'PARTIAL': 'FALSE', 'ACCESSION': 'AB019439'}) OrderedDict({'ID': 'TRAV11*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'P', 'PARTIAL': 'FALSE', 'ACCESSION': 'AE000659'}) OrderedDict({'ID': 'IGHV1-18*01'}) OrderedDict({'ID': 'IGHV1-69*07'}) OrderedDict({'ID': 'IGHV(III)-22-2*01'}) OrderedDict({'ID': 'TRAV11*01'}) <- test_convertIMGTHeader() 0.000 -> test_convertIlluminaHeader() OrderedDict({'ID': 'MISEQ:132:000000000-A2F3U:1:1101:14340:1555', 'INDEX': 'ATCACG', 'READ': '1'}) OrderedDict({'ID': 'HWI-EAS209_0006_FC706VJ:5:58:5894:21141', 'INDEX': 'ATCACG', 'READ': '1'}) OrderedDict({'ID': 'MS6_33112:1:1101:18371:1066', 'READ': '1'}) <- test_convertIlluminaHeader() 0.000 -> test_convertSRAHeader() OrderedDict({'ID': 'SRR001666.1', 'DESC': '071112_SLXA-EAS1_s_7:5:1:817:345', 'LENGTH': '36'}) OrderedDict({'ID': 'SRR735691.1', 'DESC': 'GXGJ56Z01AE06X', 'LENGTH': '222'}) OrderedDict({'ID': 'SRR1383326.1', 'DESC': '1', 'LENGTH': '250'}) OrderedDict({'ID': 'SRR1383326.1', 'READ': '2', 'DESC': '1', 'LENGTH': '250'}) OrderedDict({'ID': 'ERR346596.6', 'DESC': 'BS-DSFCONTROL04:4:000000000-A3F0Y:1:1101:13220:1649/1'}) <- test_convertSRAHeader() 0.000 -> test_calculateDistances() <- test_calculateDistances() 0.001 -> test_countMismatches() <- test_countMismatches() 0.001 -> test_initializeMismatchDictionary() <- test_initializeMismatchDictionary() 0.000 -> test_getFileType() <- test_getFileType() 0.000 -> test_extractAlignment() SEQ1> SEQ> CCACGTTTTAGTAATTAATA ALN-SEQ> CCACGTTTTAGT ALN-PR> ----GTTTTAGT PRIMER> GTTTTAGT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ2> SEQ> CCNCGTTTTAGTAATTAATA ALN-SEQ> CCNCGTTTTAGT ALN-PR> ----GTTTTAGT PRIMER> GTTTTAGT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ3> SEQ> GGGCGTTTTAGTAATTAATA ALN-SEQ> GGGCGTTTTAGT ALN-PR> ----GTTTTAGT PRIMER> GTTTTAGT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTTACT ALN-PR> ----GTTTTACT PRIMER> GTTTTACT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNNACT ALN-PR> ----NNNNNACT PRIMER> NNNNNACT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNNACT ALN-PR> ----TANNNACT PRIMER> TANNNACT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> NNNNNNNNNNNN ALN-PR> ----NNNNNNNN PRIMER> NNNNNNNN START> 4 END> 12 GAPS> 0 ERROR> 0.000000 <- test_extractAlignment() 0.000 -> test_localAlignment() TEST Ns> SEQ1> SEQ> CCACGTTTTAGTAATTAATA ALN-SEQ> CCACGTTTTAGTAATTAATA ALN-PR> -CACGTTTT----------- PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ2> SEQ> CCNCGTTTTAGTAATTAATA ALN-SEQ> CCNCGTTTTAGTAATTAATA ALN-PR> -CACGTTTT----------- PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.125000 ok test_maskSeq (tests.test_MaskPrimers.TestMaskPrimers.test_maskSeq) ... ok test_scoreAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_scoreAlignment) ... ok test_calculateSetError (tests.test_Sequence.TestSequence.test_calculateSetError) ... ok test_filterQuality (tests.test_Sequence.TestSequence.test_filterQuality) ... ok test_meanQuality (tests.test_Sequence.TestSequence.test_meanQuality) ... ok test_scoreDNA (tests.test_Sequence.TestSequence.test_scoreDNA) ... ok test_scoreSeqPair (tests.test_Sequence.TestSequence.test_scoreSeqPair) ... SEQ3> SEQ> GGGCGTTTTAGTAATTAATA ALN-SEQ> GGGCGTTTTAGTAATTAATA ALN-PR> -GGCGTTTT----------- PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTTACTAATTAATA ALN-PR> GGC-GTTTT----------- PRIMER> PR2 START> 0 END> 9 GAPS> 1 ERROR> 0.250000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNNACTAATTAATA ALN-PR> ------------ANATAA-- PRIMER> PR3 START> 12 END> 18 GAPS> 0 ERROR> 0.375000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNNACTAATTAATA ALN-PR> -GGANA-------------- PRIMER> PR3 START> 1 END> 6 GAPS> 0 ERROR> 0.375000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> None ALN-PR> None PRIMER> None START> None END> None GAPS> 0 ERROR> 1.000000 TEST INDELS> SEQ1> SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG ALN-SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG ALN-PR> ---------------ATACGTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 15 END> 38 GAPS> 0 ERROR> 0.083333 SEQ2> SEQ> CGGATCTTCTACTCAAAACCGTCCTCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG ALN-SEQ> CGGATCTTCTACTCAAAACCGTCC-TCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG ALN-PR> --------------AATAC-GTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 14 END> 38 GAPS> 2 ERROR> 0.208333 SEQ3> SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTGATCTGTTTTACATGGGGGCATCACCCAG ALN-SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTG-ATCTGTTTTACATGGGGGCATCACCCAG ALN-PR> ---------------AATACGTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 15 END> 38 GAPS> 1 ERROR> 0.125000 SEQ4> SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT ALN-SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT ALN-PR> ------CATCT-TCCTCTA------------------------------------------- PRIMER> PR2 START> 6 END> 19 GAPS> 1 ERROR> 0.250000 SEQ5> SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG ALN-SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG ALN-PR> ------CATCTTCCTCTA-------------------------------------------- PRIMER> PR2 START> 6 END> 18 GAPS> 0 ERROR> 0.166667 SEQ6> SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA ALN-SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA ALN-PR> TCT-TCCTCTA--------------------------------------------------- PRIMER> PR2 START> 0 END> 11 GAPS> 1 ERROR> 0.250000 SEQ7> SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> --GTGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 2 END> 15 GAPS> 1 ERROR> 0.083333 SEQ8> SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 3 END> 15 GAPS> 1 ERROR> 0.166667 SEQ9> SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 3 END> 15 GAPS> 1 ERROR> 0.333333 SEQ10> SEQ> -------------------------------------------------------------- ALN-SEQ> None ALN-PR> None PRIMER> None START> None END> None GAPS> 0 ERROR> 1.000000 <- test_localAlignment() 0.024 -> test_maskSeq() TEST CUT> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> AGTAATTAATA TEST MASK> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> NNNNNNAGTAATTAATA TEST TRIM> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> CGTTTTAGTAATTAATA TEST TAG> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> CCACGTTTTAGTAATTAATA <- test_maskSeq() 0.001 -> test_scoreAlignment() SEQ1> SEQ> CCACGTTTTAGTAATTAATA ALN-SEQ> CCACGTTTT ALN-PR> -CACGTTTT PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ2> SEQ> CCNCGTTTTAGTAATTAATA ALN-SEQ> CCNCGTTTT ALN-PR> -CACGTTTT PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.125000 SEQ3> SEQ> GGGCGTTTTAGTAATTAATA ALN-SEQ> GGGCGTTTT ALN-PR> -GGCGTTTT PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTT ALN-PR> -GGCGTTTT PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.250000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNN ALN-PR> -GGCGTTTT PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.750000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNN ALN-PR> -GGANATAA PRIMER> PR3 START> 1 END> 9 GAPS> 0 ERROR> 0.375000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> NNNNNNNNN ALN-PR> -CACGTTTT PRIMER> None START> 1 END> 9 GAPS> 0 ERROR> 1.000000 <- test_scoreAlignment() 0.007 -> test_calculateSetError() REF> CGGCGTAA 0.4347826086956522 REF> NNNNNNNN 1.0 <- test_calculateSetError() 0.000 -> test_filterQuality() RESULT> True 25 RESULT> False 5 RESULT> False 0 <- test_filterQuality() 0.000 -> test_meanQuality() RESULT> 25 [30, 30, 20, 20, 30, 30, 40, 40] RESULT> 5 [30, 30, 0, 0, 30, 30, 20, 20] RESULT> 0 [0, 0, 0, 0, 0, 0, 0, 0] <- test_meanQuality() 0.000 -> test_scoreDNA() Default DNA Scores> A==A> 1 A==T> 0 A==R> 1 U==T> 1 A==N> 1 N==A> 1 A==-> 0 -==A> 0 Symmetric DNA Scores> A==A> 1 A==T> 0 A==R> 1 U==T> 1 A==N> 1 N==A> 1 A==-> 1 -==A> 1 Asymmetric DNA Scores> A==A> 1 A==T> 0 A==R> 1 U==T> 1 A==N> 1 N==A> 0 A==-> 1 -==A> 0 <- test_scoreDNA() 0.000 -> test_scoreSeqPair() Default DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ6> NNNNNNAA SEQ7> --------ok test_weightDNA (tests.test_Sequence.TestSequence.test_weightDNA) ... ok test_consensusUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_consensusUnify) ... ok test_deletionUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_deletionUnify) ... ok ---------------------------------------------------------------------- Ran 40 tests in 0.097s OK (skipped=6) SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ7> -------- SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 Asymmetric DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 3 WEIGHT> 8 ERROR> 0.625000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ7> -------- SEQ8> CG------ SCORE> 0 WEIGHT> 8 ERROR> 1.000000 Masked DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 5 WEIGHT> 6 ERROR> 0.166667 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 3 WEIGHT> 6 ERROR> 0.500000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 2 WEIGHT> 2 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 3 WEIGHT> 6 ERROR> 0.500000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 4 WEIGHT> 6 ERROR> 0.333333 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 1 WEIGHT> 2 ERROR> 0.500000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 0 WEIGHT> 6 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 2 WEIGHT> 6 ERROR> 0.666667 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 6 ERROR> 0.166667 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 2 WEIGHT> 2 ERROR> 0.000000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 1 WEIGHT> 2 ERROR> 0.500000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 2 WEIGHT> 6 ERROR> 0.666667 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 6 ERROR> 0.333333 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ7> -------- SCORE> 0 WEIGHT> 2 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 0 WEIGHT> 2 ERROR> 1.000000 SEQ7> -------- SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 <- test_scoreSeqPair() 0.006 -> test_weightDNA() DNA Weight> SEQ1> 8 SEQ2> 6 SEQ3> 8 SEQ4> 6 SEQ5> 0 SEQ6> 2 SEQ7> 8 SEQ8> 8 AA Weight> SEQ1> 8 SEQ2> 6 SEQ3> 8 SEQ4> 6 <- test_weightDNA() 0.000 -> test_consensusUnify() ID> SEQ0|BARCODE=AAAA|SAMPLE=S1 -> SEQ0|BARCODE=AAAA|SAMPLE=S1 ID> SEQ1|BARCODE=AAAA|SAMPLE=S1 -> SEQ1|BARCODE=AAAA|SAMPLE=S1 ID> SEQ2|BARCODE=AAAA|SAMPLE=S2 -> SEQ2|BARCODE=AAAA|SAMPLE=S1 ID> SEQ3|BARCODE=AAAA|SAMPLE=S3 -> SEQ3|BARCODE=AAAA|SAMPLE=S1 ID> SEQ4|BARCODE=CCCC|SAMPLE=S1 -> SEQ4|BARCODE=CCCC|SAMPLE=S1 ID> SEQ5|BARCODE=CCCC|SAMPLE=S2 -> SEQ5|BARCODE=CCCC|SAMPLE=S1 ID> SEQ6|BARCODE=GGGG|SAMPLE=S2 -> SEQ6|BARCODE=GGGG|SAMPLE=S2 ID> SEQ7|BARCODE=GGGG|SAMPLE=S2 -> SEQ7|BARCODE=GGGG|SAMPLE=S2 <- test_consensusUnify() 0.000 -> test_deletionUnify() ID> SEQ0|BARCODE=AAAA|SAMPLE=S1 -> False ID> SEQ1|BARCODE=AAAA|SAMPLE=S1 -> False ID> SEQ2|BARCODE=AAAA|SAMPLE=S2 -> False ID> SEQ3|BARCODE=AAAA|SAMPLE=S3 -> False ID> SEQ4|BARCODE=CCCC|SAMPLE=S1 -> False ID> SEQ5|BARCODE=CCCC|SAMPLE=S2 -> False ID> SEQ6|BARCODE=GGGG|SAMPLE=S2 -> True ID> SEQ7|BARCODE=GGGG|SAMPLE=S2 -> True <- test_deletionUnify() 0.000 create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py install --root /build/reproducible-path/presto-0.7.2/debian/python3-presto running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_scripts running install_lib creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/UnifyHeaders.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/MaskPrimers.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/EstimateError.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/ConvertHeaders.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/CollapseSeq.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/ClusterSets.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/BuildConsensus.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/AssemblePairs.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/UnifyHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/SplitSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/ParseLog.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/ParseHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/PairSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/MaskPrimers.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/FilterSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/EstimateError.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/ConvertHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/CollapseSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/ClusterSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/BuildConsensus.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/AssemblePairs.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/AlignSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Multiprocessing.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Sequence.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Applications.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Commandline.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/IO.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Annotation.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Defaults.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Version.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Annotation.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Applications.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Commandline.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Defaults.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/IO.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Multiprocessing.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Sequence.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Version.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__init__.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/UnifyHeaders.py to UnifyHeaders.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/SplitSeq.py to SplitSeq.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/ParseLog.py to ParseLog.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/ParseHeaders.py to ParseHeaders.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/PairSeq.py to PairSeq.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/MaskPrimers.py to MaskPrimers.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/FilterSeq.py to FilterSeq.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/EstimateError.py to EstimateError.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/ConvertHeaders.py to ConvertHeaders.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/CollapseSeq.py to CollapseSeq.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/ClusterSets.py to ClusterSets.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/BuildConsensus.py to BuildConsensus.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/AssemblePairs.py to AssemblePairs.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/AlignSets.py to AlignSets.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Annotation.py to Annotation.cpython-313.pyc /usr/lib/python3.13/dist-packages/presto/Annotation.py:293: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.13/dist-packages/presto/Annotation.py:368: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.13/dist-packages/presto/Annotation.py:491: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.13/dist-packages/presto/Annotation.py:493: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.13/dist-packages/presto/Annotation.py:494: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Applications.py to Applications.cpython-313.pyc /usr/lib/python3.13/dist-packages/presto/Applications.py:61: SyntaxWarning: invalid escape sequence '\.' /usr/lib/python3.13/dist-packages/presto/Applications.py:288: SyntaxWarning: invalid escape sequence '\>' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Commandline.py to Commandline.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Defaults.py to Defaults.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/IO.py to IO.cpython-313.pyc /usr/lib/python3.13/dist-packages/presto/IO.py:34: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Multiprocessing.py to Multiprocessing.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Sequence.py to Sequence.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Version.py to Version.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__init__.py to __init__.cpython-313.pyc running install_egg_info running egg_info creating presto.egg-info writing presto.egg-info/PKG-INFO writing dependency_links to presto.egg-info/dependency_links.txt writing requirements to presto.egg-info/requires.txt writing top-level names to presto.egg-info/top_level.txt writing manifest file 'presto.egg-info/SOURCES.txt' reading manifest file 'presto.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'presto.egg-info/SOURCES.txt' Copying presto.egg-info to /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto-0.7.2.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/UnifyHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/SplitSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/ParseLog.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/ParseHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/PairSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/MaskPrimers.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/FilterSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/EstimateError.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/ConvertHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/CollapseSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/ClusterSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/BuildConsensus.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/AssemblePairs.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/AlignSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/UnifyHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/SplitSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ParseLog.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ParseHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/PairSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/MaskPrimers.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/FilterSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/EstimateError.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ConvertHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/CollapseSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ClusterSets.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/BuildConsensus.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/AssemblePairs.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/AlignSets.py to 755 I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/presto-0.7.2/debian/python3-presto running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_scripts running install_lib creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/UnifyHeaders.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/MaskPrimers.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/EstimateError.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/ConvertHeaders.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/CollapseSeq.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/ClusterSets.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/BuildConsensus.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/AssemblePairs.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/UnifyHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/SplitSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/ParseLog.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/ParseHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/PairSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/MaskPrimers.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/FilterSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/EstimateError.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/ConvertHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/CollapseSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/ClusterSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/BuildConsensus.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/AssemblePairs.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/AlignSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Multiprocessing.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Sequence.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Applications.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Commandline.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/IO.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Annotation.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Defaults.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Version.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Applications.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Commandline.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Defaults.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/IO.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Multiprocessing.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Sequence.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Version.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__init__.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/UnifyHeaders.py to UnifyHeaders.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/SplitSeq.py to SplitSeq.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/ParseLog.py to ParseLog.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/ParseHeaders.py to ParseHeaders.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/PairSeq.py to PairSeq.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/MaskPrimers.py to MaskPrimers.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/FilterSeq.py to FilterSeq.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/EstimateError.py to EstimateError.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/ConvertHeaders.py to ConvertHeaders.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/CollapseSeq.py to CollapseSeq.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/ClusterSets.py to ClusterSets.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/BuildConsensus.py to BuildConsensus.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/AssemblePairs.py to AssemblePairs.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/AlignSets.py to AlignSets.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Annotation.py to Annotation.cpython-312.pyc /usr/lib/python3.12/dist-packages/presto/Annotation.py:293: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/presto/Annotation.py:368: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/presto/Annotation.py:491: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/presto/Annotation.py:493: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/presto/Annotation.py:494: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Applications.py to Applications.cpython-312.pyc /usr/lib/python3.12/dist-packages/presto/Applications.py:61: SyntaxWarning: invalid escape sequence '\.' /usr/lib/python3.12/dist-packages/presto/Applications.py:288: SyntaxWarning: invalid escape sequence '\>' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Commandline.py to Commandline.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Defaults.py to Defaults.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/IO.py to IO.cpython-312.pyc /usr/lib/python3.12/dist-packages/presto/IO.py:34: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Multiprocessing.py to Multiprocessing.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Sequence.py to Sequence.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Version.py to Version.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__init__.py to __init__.cpython-312.pyc running install_egg_info running egg_info writing presto.egg-info/PKG-INFO writing dependency_links to presto.egg-info/dependency_links.txt writing requirements to presto.egg-info/requires.txt writing top-level names to presto.egg-info/top_level.txt reading manifest file 'presto.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'presto.egg-info/SOURCES.txt' Copying presto.egg-info to /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto-0.7.2.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.12/UnifyHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/SplitSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/ParseLog.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/ParseHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/PairSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/MaskPrimers.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/FilterSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/EstimateError.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/ConvertHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/CollapseSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/ClusterSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/BuildConsensus.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/AssemblePairs.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/AlignSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/UnifyHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/SplitSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ParseLog.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ParseHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/PairSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/MaskPrimers.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/FilterSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/EstimateError.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ConvertHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/CollapseSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ClusterSets.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/BuildConsensus.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/AssemblePairs.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/AlignSets.py to 755 debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/presto-0.7.2' dh_install mkdir -p debian/presto/usr mv debian/python3-presto/usr/bin debian/presto/usr make[1]: Leaving directory '/build/reproducible-path/presto-0.7.2' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/presto-0.7.2' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/presto-0.7.2' dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-presto' in '../python3-presto_0.7.2-1_arm64.deb'. dpkg-deb: building package 'presto' in '../presto_0.7.2-1_all.deb'. dpkg-genbuildinfo --build=binary -O../presto_0.7.2-1_arm64.buildinfo dpkg-genchanges --build=binary -O../presto_0.7.2-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from presto-0.7.2/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2142681 and its subdirectories I: Current time: Wed Dec 24 12:11:57 -12 2025 I: pbuilder-time-stamp: 1766621517 Thu Nov 21 17:48:59 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Thu Nov 21 17:48:59 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Thu Nov 21 17:48:59 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Thu Nov 21 17:48:59 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-93Fon1' ==================================================================================== Thu Nov 21 17:49:00 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "2 presto unstable /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q 0.7.2-1" as arguments. Thu Nov 21 17:49:00 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-QhWHI0V6" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Nov 21 17:49:00 UTC 2024 I: Downloading source for unstable/presto=0.7.2-1 Reading package lists... NOTICE: 'presto' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/presto.git Please use: git clone https://salsa.debian.org/med-team/presto.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 385 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main presto 0.7.2-1 (dsc) [2233 B] Get:2 http://deb.debian.org/debian unstable/main presto 0.7.2-1 (tar) [362 kB] Get:3 http://deb.debian.org/debian unstable/main presto 0.7.2-1 (diff) [20.8 kB] Fetched 385 kB in 0s (29.5 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'presto' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/presto.git Please use: git clone https://salsa.debian.org/med-team/presto.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 385 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main presto 0.7.2-1 (dsc) [2233 B] Get:2 http://deb.debian.org/debian unstable/main presto 0.7.2-1 (tar) [362 kB] Get:3 http://deb.debian.org/debian unstable/main presto 0.7.2-1 (diff) [20.8 kB] Fetched 385 kB in 0s (29.5 MB/s) Download complete and in download only mode ============================================================================= Re-Building presto in unstable on arm64 on codethink04-arm64 now. Date: Thu Nov 21 17:49:01 GMT 2024 Date UTC: Thu Nov 21 17:49:01 UTC 2024 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/pbuilderrc_N9g3 + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' presto = debian-installer -o presto = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' presto = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/pbuilderrc_N9g3 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/b2 --logfile b2/build.log presto_0.7.2-1.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Nov 22 07:49:01 +14 2024 I: pbuilder-time-stamp: 1732211341 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 [presto_0.7.2-1.dsc] I: copying [./presto_0.7.2.orig.tar.xz] I: copying [./presto_0.7.2-1.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Feb 19 12:51:18 2024 gpgv: using RSA key 4A31DB5A1EE4096C87399880903649294C33F9B7 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./presto_0.7.2-1.dsc: no acceptable signature found dpkg-source: info: extracting presto in presto-0.7.2 dpkg-source: info: unpacking presto_0.7.2.orig.tar.xz dpkg-source: info: unpacking presto_0.7.2-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1028729/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Nov 21 17:49 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1028729/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1028729/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=e1fddef8a19c4e94b993c20ab9ab36e8 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1028729 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/pbuilderrc_N9g3 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/b2 --logfile b2/build.log presto_0.7.2-1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1028729/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: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all, python3-setuptools, python3-biopython, python3-pandas, python3-scipy, python3-packaging, vsearch, cd-hit dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20084 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-packaging; however: Package python3-packaging is not installed. pbuilder-satisfydepends-dummy depends on vsearch; however: Package vsearch is not installed. pbuilder-satisfydepends-dummy depends on cd-hit; however: Package cd-hit 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: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cd-hit{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{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} libxml2{a} libxrender1{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-autocommand{a} python3-biopython{a} python3-cairo{a} python3-chardet{a} python3-dateutil{a} python3-decorator{a} python3-freetype{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pkg-resources{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} vsearch{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra krb5-locales libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-bottleneck python3-bs4 python3-html5lib python3-jinja2 python3-lxml python3-matplotlib python3-numexpr python3-odf python3-olefile python3-openpyxl python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 132 newly installed, 0 to remove and 0 not upgraded. Need to get 91.9 MB of archives. After unpacking 419 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.7-3 [808 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.7-3 [1940 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.7-1 [26.8 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 12 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.7-3 [1902 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.7-1 [9708 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.7-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.0-2 [850 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.0-2 [1838 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 cd-hit arm64 4.8.1-4+b1 [509 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 48 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 62 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.2.0-1 [731 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20241024 [109 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1+b1 [22.5 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 78 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b2 [27.2 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.2-3 [1411 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b2 [25.6 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.0-2+b4 [185 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [1922 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.1-1+b2 [13.8 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libwebpdemux2 arm64 1.4.0-0.1+b1 [110 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.4.0-0.1+b1 [122 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.0-2 [730 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.12.7-1 [1052 B] Get: 115 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [3816 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 python3-pil arm64 10.4.0-1+b1 [498 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 python3-cairo arm64 1.26.1-2+b1 [130 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 121 http://deb.debian.org/debian unstable/main arm64 python3-reportlab all 4.2.5-1 [1117 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 python3-biopython arm64 1.84+dfsg-4+b1 [1644 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 python3-tz all 2024.1-2 [30.9 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-5+b1 [6028 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 python3-scipy arm64 1.13.1-6 [18.2 MB] Get: 132 http://deb.debian.org/debian unstable/main arm64 vsearch arm64 2.29.1-1 [410 kB] Fetched 91.9 MB in 1s (65.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (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 ... 20084 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.7-3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_arm64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:arm64 (3.12.7-3) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20404 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_arm64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_arm64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21466 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_arm64.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../001-libpython3.13-minimal_3.13.0-2_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../002-python3.13-minimal_3.13.0-2_arm64.deb ... Unpacking python3.13-minimal (3.13.0-2) ... Selecting previously unselected package sgml-base. Preparing to unpack .../003-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../006-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../009-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../012-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... 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Unpacking cd-hit (4.8.1-4+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../020-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../021-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../022-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../023-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../024-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../025-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../026-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../027-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../028-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../029-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../030-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../031-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../032-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../033-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../034-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../035-python3-more-itertools_10.5.0-1_all.deb ... Unpacking python3-more-itertools (10.5.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../036-python3-typing-extensions_4.12.2-2_all.deb ... Unpacking python3-typing-extensions (4.12.2-2) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../037-python3-typeguard_4.4.1-1_all.deb ... Unpacking python3-typeguard (4.4.1-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../038-python3-inflect_7.3.1-2_all.deb ... Unpacking python3-inflect (7.3.1-2) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../039-python3-jaraco.context_6.0.0-1_all.deb ... Unpacking python3-jaraco.context (6.0.0-1) ... Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../040-python3-jaraco.functools_4.1.0-1_all.deb ... Unpacking python3-jaraco.functools (4.1.0-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../041-python3-pkg-resources_75.2.0-1_all.deb ... Unpacking python3-pkg-resources (75.2.0-1) ... Selecting previously unselected package python3-jaraco.text. 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Setting up libgraphite2-3:arm64 (1.3.14-2+b1) ... Setting up liblcms2-2:arm64 (2.16-2) ... Setting up libpixman-1-0:arm64 (0.44.0-3) ... Setting up libsharpyuv0:arm64 (1.4.0-0.1+b1) ... Setting up libxau6:arm64 (1:1.0.11-1) ... Setting up libxdmcp6:arm64 (1:1.1.5-1) ... Setting up libkeyutils1:arm64 (1.6.3-4) ... Setting up libxcb1:arm64 (1.17.0-2+b1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-5) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libxcb-render0:arm64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up vsearch (2.29.1-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:arm64 (1.1.0-2+b6) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libdeflate0:arm64 (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ... Setting up libcom-err2:arm64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Nov 21 17:50:18 UTC 2024. Universal Time is now: Thu Nov 21 17:50:18 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... Setting up libfontenc1:arm64 (1:1.1.8-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.82.2-3) ... No schema files found: doing nothing. Setting up libblas3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.15-1) ... Setting up libimagequant0:arm64 (2.18.0-1+b2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-2) ... Setting up autopoint (0.22.5-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libgfortran5:arm64 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:arm64 (1.4.0-0.1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:arm64 (4.5.1+git230720-5) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libopenjp2-7:arm64 (2.5.0-2+b4) ... Setting up python3.13-minimal (3.13.0-2) ... Setting up libx11-6:arm64 (2:1.8.10-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libwebpmux3:arm64 (1.4.0-0.1+b1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b2) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libwebpdemux2:arm64 (1.4.0-0.1+b1) ... Setting up libxext6:arm64 (2:1.3.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libreadline8t64:arm64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:arm64 (10.0.1-1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1+b1) ... Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1+b2) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Setting up python3.13 (3.13.0-2) ... Setting up po-debconf (1.0.21+nmu1) ... 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:arm64 (1.18.2-2) ... Setting up libraqm0:arm64 (0.10.1-1+b2) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up libpython3.12-stdlib:arm64 (3.12.7-3) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libpython3-stdlib:arm64 (3.12.7-1) ... Setting up python3 (3.12.7-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-tz (2024.1-2) ... Setting up python3-pil:arm64 (10.4.0-1+b1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.2-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-cairo (1.26.1-2+b1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-all (3.12.7-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up python3-reportlab (4.2.5-1) ... Setting up dh-python (6.20241024) ... Setting up python3-scipy (1.13.1-6) ... Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5+b1) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.84+dfsg-4+b1) ... 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: user script /srv/workspace/pbuilder/1028729/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/1028729/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/presto-0.7.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../presto_0.7.2-1_source.changes dpkg-buildpackage: info: source package presto dpkg-buildpackage: info: source version 0.7.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Lance Lin dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 dpkg-source: info: using options from presto-0.7.2/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean running clean removing '/build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it I: pybuild base:311: python3.12 setup.py clean running clean removing '/build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config running config I: pybuild base:311: python3.12 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py build running build running build_py creating /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/__init__.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Version.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Sequence.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Multiprocessing.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/IO.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Defaults.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Commandline.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Applications.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Annotation.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto running build_scripts creating build/scripts-3.13 copying and adjusting bin/AlignSets.py -> build/scripts-3.13 copying and adjusting bin/AssemblePairs.py -> build/scripts-3.13 copying and adjusting bin/BuildConsensus.py -> build/scripts-3.13 copying and adjusting bin/ClusterSets.py -> build/scripts-3.13 copying and adjusting bin/CollapseSeq.py -> build/scripts-3.13 copying and adjusting bin/ConvertHeaders.py -> build/scripts-3.13 copying and adjusting bin/EstimateError.py -> build/scripts-3.13 copying and adjusting bin/FilterSeq.py -> build/scripts-3.13 copying and adjusting bin/MaskPrimers.py -> build/scripts-3.13 copying and adjusting bin/PairSeq.py -> build/scripts-3.13 copying and adjusting bin/ParseHeaders.py -> build/scripts-3.13 copying and adjusting bin/ParseLog.py -> build/scripts-3.13 copying and adjusting bin/SplitSeq.py -> build/scripts-3.13 copying and adjusting bin/UnifyHeaders.py -> build/scripts-3.13 changing mode of build/scripts-3.13/AlignSets.py from 644 to 755 changing mode of build/scripts-3.13/AssemblePairs.py from 644 to 755 changing mode of build/scripts-3.13/BuildConsensus.py from 644 to 755 changing mode of build/scripts-3.13/ClusterSets.py from 644 to 755 changing mode of build/scripts-3.13/CollapseSeq.py from 644 to 755 changing mode of build/scripts-3.13/ConvertHeaders.py from 644 to 755 changing mode of build/scripts-3.13/EstimateError.py from 644 to 755 changing mode of build/scripts-3.13/FilterSeq.py from 644 to 755 changing mode of build/scripts-3.13/MaskPrimers.py from 644 to 755 changing mode of build/scripts-3.13/PairSeq.py from 644 to 755 changing mode of build/scripts-3.13/ParseHeaders.py from 644 to 755 changing mode of build/scripts-3.13/ParseLog.py from 644 to 755 changing mode of build/scripts-3.13/SplitSeq.py from 644 to 755 changing mode of build/scripts-3.13/UnifyHeaders.py from 644 to 755 I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/__init__.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Version.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Sequence.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Multiprocessing.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/IO.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Defaults.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Commandline.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Applications.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Annotation.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto running build_scripts creating build/scripts-3.12 copying and adjusting bin/AlignSets.py -> build/scripts-3.12 copying and adjusting bin/AssemblePairs.py -> build/scripts-3.12 copying and adjusting bin/BuildConsensus.py -> build/scripts-3.12 copying and adjusting bin/ClusterSets.py -> build/scripts-3.12 copying and adjusting bin/CollapseSeq.py -> build/scripts-3.12 copying and adjusting bin/ConvertHeaders.py -> build/scripts-3.12 copying and adjusting bin/EstimateError.py -> build/scripts-3.12 copying and adjusting bin/FilterSeq.py -> build/scripts-3.12 copying and adjusting bin/MaskPrimers.py -> build/scripts-3.12 copying and adjusting bin/PairSeq.py -> build/scripts-3.12 copying and adjusting bin/ParseHeaders.py -> build/scripts-3.12 copying and adjusting bin/ParseLog.py -> build/scripts-3.12 copying and adjusting bin/SplitSeq.py -> build/scripts-3.12 copying and adjusting bin/UnifyHeaders.py -> build/scripts-3.12 changing mode of build/scripts-3.12/AlignSets.py from 644 to 755 changing mode of build/scripts-3.12/AssemblePairs.py from 644 to 755 changing mode of build/scripts-3.12/BuildConsensus.py from 644 to 755 changing mode of build/scripts-3.12/ClusterSets.py from 644 to 755 changing mode of build/scripts-3.12/CollapseSeq.py from 644 to 755 changing mode of build/scripts-3.12/ConvertHeaders.py from 644 to 755 changing mode of build/scripts-3.12/EstimateError.py from 644 to 755 changing mode of build/scripts-3.12/FilterSeq.py from 644 to 755 changing mode of build/scripts-3.12/MaskPrimers.py from 644 to 755 changing mode of build/scripts-3.12/PairSeq.py from 644 to 755 changing mode of build/scripts-3.12/ParseHeaders.py from 644 to 755 changing mode of build/scripts-3.12/ParseLog.py from 644 to 755 changing mode of build/scripts-3.12/SplitSeq.py from 644 to 755 changing mode of build/scripts-3.12/UnifyHeaders.py from 644 to 755 dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: cp -r /build/reproducible-path/presto-0.7.2/bin /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build; I: pybuild base:311: cd /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build; python3.13 -m unittest discover -v /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Annotation.py:293: SyntaxWarning: invalid escape sequence '\s' sub_regex = '[%s\s]+' % re.escape(''.join(delimiter)) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Annotation.py:368: SyntaxWarning: invalid escape sequence '\s' sub_regex = '[%s\s]+' % re.escape(''.join(delimiter[1:])) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Annotation.py:491: SyntaxWarning: invalid escape sequence '\s' header['SPECIES'] = re.sub('\s', '_', fields[2]) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Annotation.py:493: SyntaxWarning: invalid escape sequence '\(' header['FUNCTIONALITY'] = re.sub('[\(\)\[\]]', '', fields[3]) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Annotation.py:494: SyntaxWarning: invalid escape sequence '\s' header['PARTIAL'] = 'FALSE' if re.sub('\s', '', fields[13]) == '' else 'TRUE' /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/IO.py:34: SyntaxWarning: invalid escape sequence '\s' if replace_special: parse_id = lambda x: re.sub('[\s,=|]+', '_', x) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Applications.py:61: SyntaxWarning: invalid escape sequence '\.' version = re.sub('\.linux.*$','',version) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Applications.py:288: SyntaxWarning: invalid escape sequence '\>' id_regex = re.compile('([0-9]+\t[0-9]+nt, \>)(.+)(\.\.\.)') test_collapseAnnotation (tests.test_Annotation.TestAnnotation.test_collapseAnnotation) ... ok test_getCoordKey (tests.test_Annotation.TestAnnotation.test_getCoordKey) ... ok test_mergeAnnotation (tests.test_Annotation.TestAnnotation.test_mergeAnnotation) ... ok test_renameAnnotation (tests.test_Annotation.TestAnnotation.test_renameAnnotation) ... ok test_alignAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_alignAssembly) ... skipped '-> alignAssembly() skipped\n' test_makeBlastnDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeBlastnDb) ... skipped '-> makeBlastnDb() skipped\n' test_makeUSearchDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeUSearchDb) ... skipped '-> makeUSearchDb() skipped\n' test_referenceAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_referenceAssembly) ... skipped '-> referenceAssembly() skipped\n' test_runBlastn (tests.test_AssemblePairs.TestAssemblePairs.test_runBlastn) ... skipped '-> runBlastn() skipped\n' test_runUSearch (tests.test_AssemblePairs.TestAssemblePairs.test_runUSearch) ... skipped '-> runUSearch() skipped\n' test_calculateSetError (tests.test_BuildConsensus.TestBuildConsensus.test_calculateSetError) ... ok test_deleteSeqPositions (tests.test_BuildConsensus.TestBuildConsensus.test_deleteSeqPositions) ... ok test_findGapPositions (tests.test_BuildConsensus.TestBuildConsensus.test_findGapPositions) ... ok test_frequencyConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_frequencyConsensus) ... ok test_qualityConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_qualityConsensus) ... ok test_runCDHit (tests.test_ClusterSets.TestClusterSets.test_runCDHit) ... ok test_runUClust (tests.test_ClusterSets.TestClusterSets.test_runUClust) ... ok test_checkSeqEqual (tests.test_CollapseSeq.TestCollapseSeq.test_checkSeqEqual) ... ok test_convert454Header (tests.test_ConvertHeaders.TestConvertHeaders.test_convert454Header) ... ok test_convertGenbankHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertGenbankHeader) ... ok test_convertGenericHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertGenericHeader) ... ok test_convertIMGTHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertIMGTHeader) ... ok test_convertIlluminaHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertIlluminaHeader) ... ok test_convertSRAHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertSRAHeader) ... ok test_calculateDistances (tests.test_EstimateError.TestEstimateError.test_calculateDistances) ... /usr/lib/python3/dist-packages/Bio/SeqRecord.py:228: BiopythonDeprecationWarning: Using a string as the sequence is deprecated and will raise a TypeError in future. It has been converted to a Seq object. warnings.warn( ok test_countMismatches (tests.test_EstimateError.TestEstimateError.test_countMismatches) ... ok test_initializeMismatchDictionary (tests.test_EstimateError.TestEstimateError.test_initializeMismatchDictionary) ... ok test_getFileType (tests.test_IO.TestIO.test_getFileType) ... ok test_extractAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_extractAlignment) ... ok test_localAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_localAlignment) ... -> test_collapseAnnotation() OrderedDict({'ID': 'SEQ1', 'TEST1': 'A', 'TEST2': 1, 'TEST3': 'First'}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'B', 'TEST2': 2, 'TEST3': 'Second'}) OrderedDict({'ID': 'SEQ1', 'TEST1': ['A', 'B'], 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'AB', 'TEST2': '12', 'TEST3': 'FirstSecond'}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '1', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '2', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '3', 'TEST3': ['First', 'Second']}) <- test_collapseAnnotation() 0.000 -> test_getCoordKey() ['MISEQ:132:000000000-A2F3U:1:1101:14340:1555', 'HWI-EAS209_0006_FC706VJ:5:58:5894:21141', 'MS6_33112:1:1101:18371:1066'] ['SRR001666.1', 'SRR735691.1', 'SRR1383326.1', 'SRR1383326.1', 'ERR346596.6'] ['000034_0199_0169', 'GXGJ56Z01AE06X'] <- test_getCoordKey() 0.000 -> test_mergeAnnotation() OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,C,C', 'TEST2': '1,2,3', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'C,C,A,B', 'TEST2': '3,1,2', 'TEST3': ['First', 'Second']}) <- test_mergeAnnotation() 0.000 -> test_renameAnnotation() OrderedDict({'ID': 'SEQ1', 'RENAMED1': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'RENAMED2': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2,First,Second'}) <- test_renameAnnotation() 0.000 -> test_calculateSetError() Frequency consensus error> REF> CGGCGTAA SEQ1> CGGCGTAA SEQ2> CCNNGTAA SEQ3> CGGC--TA SEQ4> CGNN--TA SEQ5> CGGC--AA ERROR> 0.250000 Quality consensus error> REF> CGGCNNAA SEQ1> CGGCGTAA SEQ2> CCNNGTAA SEQ3> CGGC--TA SEQ4> CGNN--TA SEQ5> CGGC--AA ERROR> 0.233333 <- test_calculateSetError() 0.000 -> test_deleteSeqPositions() MAX_GAP=0.4> CGGCAA MAX_GAP=0.8> CGGCGTAA <- test_deleteSeqPositions() 0.000 -> test_findGapPositions() MAX_GAP=0.4> [4, 5] MAX_GAP=0.8> [] <- test_findGapPositions() 0.000 -> test_frequencyConsensus() MIN_FREQ=0.2> CGGCGTAA MIN_FREQ=0.8> CGGCGTNA <- test_frequencyConsensus() 0.000 -> test_qualityConsensus() MIN_QUAL=0> CGGCGTAA [90, 90, 36, 36, 16, 16, 72, 90] MIN_QUAL=20> CGGCNNAA [90, 90, 36, 36, 0, 0, 72, 90] MIN_FREQ=0.8> CGGCNNNA [90, 90, 36, 36, 0, 0, 0, 90] <- test_qualityConsensus() 0.000 -> test_runCDHit() FULL_LENGTH> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} TRIMMED> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} ZERO_LENGTH> None <- test_runCDHit() 0.068 -> test_runUClust() FULL_LENGTH> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} TRIMMED> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} ZERO_LENGTH> None <- test_runUClust() 0.086 -> test_checkSeqEqual() DNA Equality> SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA EQUAL> True SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA SEQ3|COUNT=3> CCACGTTTTACTAATTAATA EQUAL> False SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA SEQ4|COUNT=4> CCACGTTTTANTAATTAATA EQUAL> True SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA SEQ3|COUNT=3> CCACGTTTTACTAATTAATA EQUAL> False SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA SEQ4|COUNT=4> CCACGTTTTANTAATTAATA EQUAL> True SEQ3|COUNT=3> CCACGTTTTACTAATTAATA SEQ4|COUNT=4> CCACGTTTTANTAATTAATA EQUAL> True <- test_checkSeqEqual() 0.000 -> test_convert454Header() OrderedDict({'ID': '000034_0199_0169', 'LENGTH': '437', 'UACCNO': 'GNDG01201ARRCR'}) OrderedDict({'ID': 'GXGJ56Z01AE06X', 'LENGTH': '222'}) <- test_convert454Header() 0.000 -> test_convertGenbankHeader() OrderedDict({'ID': 'CM000663.2', 'GI': '568336023', 'SOURCE': 'gb', 'DESC': 'Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) OrderedDict({'ID': 'CM000663.2', 'DESC': 'Homo_sapiens_chromosome_1__GRCh38_reference_primary_assembly'}) <- test_convertGenbankHeader() 0.000 -> test_convertGenericHeader() OrderedDict({'ID': 'gi_568336023_gb_CM000663.2_Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) OrderedDict({'ID': 'CM000663.2_Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) OrderedDict({'ID': 'M99641_IGHV1-18*01_Homo_sapiens_F_V-REGION_188..483_296_nt_1_296+24_320_'}) OrderedDict({'ID': "Z29978_IGHV1-69*07_Homo_sapiens_F_V-REGION_1..233_233_nt_1_233+58_291_partial_in_5'_and_in_3'_"}) OrderedDict({'ID': 'AB019439_IGHV(III)-22-2*01_Homo_sapiens_P_L-PART1+V-EXON_168065..168119+168222..168262_96_nt_1_96+0_96_'}) OrderedDict({'ID': 'AE000659_TRAV11*01_Homo_sapiens_(P)_V-REGION_85121..85397_276_nt_1_276+42_318_'}) <- test_convertGenericHeader() 0.000 -> test_convertIMGTHeader() OrderedDict({'ID': 'IGHV1-18*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'F', 'PARTIAL': 'FALSE', 'ACCESSION': 'M99641'}) OrderedDict({'ID': 'IGHV1-69*07', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'F', 'PARTIAL': 'TRUE', 'ACCESSION': 'Z29978'}) OrderedDict({'ID': 'IGHV(III)-22-2*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'L-PART1+V-EXON', 'FUNCTIONALITY': 'P', 'PARTIAL': 'FALSE', 'ACCESSION': 'AB019439'}) OrderedDict({'ID': 'TRAV11*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'P', 'PARTIAL': 'FALSE', 'ACCESSION': 'AE000659'}) OrderedDict({'ID': 'IGHV1-18*01'}) OrderedDict({'ID': 'IGHV1-69*07'}) OrderedDict({'ID': 'IGHV(III)-22-2*01'}) OrderedDict({'ID': 'TRAV11*01'}) <- test_convertIMGTHeader() 0.000 -> test_convertIlluminaHeader() OrderedDict({'ID': 'MISEQ:132:000000000-A2F3U:1:1101:14340:1555', 'INDEX': 'ATCACG', 'READ': '1'}) OrderedDict({'ID': 'HWI-EAS209_0006_FC706VJ:5:58:5894:21141', 'INDEX': 'ATCACG', 'READ': '1'}) OrderedDict({'ID': 'MS6_33112:1:1101:18371:1066', 'READ': '1'}) <- test_convertIlluminaHeader() 0.000 -> test_convertSRAHeader() OrderedDict({'ID': 'SRR001666.1', 'DESC': '071112_SLXA-EAS1_s_7:5:1:817:345', 'LENGTH': '36'}) OrderedDict({'ID': 'SRR735691.1', 'DESC': 'GXGJ56Z01AE06X', 'LENGTH': '222'}) OrderedDict({'ID': 'SRR1383326.1', 'DESC': '1', 'LENGTH': '250'}) OrderedDict({'ID': 'SRR1383326.1', 'READ': '2', 'DESC': '1', 'LENGTH': '250'}) OrderedDict({'ID': 'ERR346596.6', 'DESC': 'BS-DSFCONTROL04:4:000000000-A3F0Y:1:1101:13220:1649/1'}) <- test_convertSRAHeader() 0.000 -> test_calculateDistances() <- test_calculateDistances() 0.001 -> test_countMismatches() <- test_countMismatches() 0.001 -> test_initializeMismatchDictionary() <- test_initializeMismatchDictionary() 0.000 -> test_getFileType() <- test_getFileType() 0.000 -> test_extractAlignment() SEQ1> SEQ> CCACGTTTTAGTAATTAATA ALN-SEQ> CCACGTTTTAGT ALN-PR> ----GTTTTAGT PRIMER> GTTTTAGT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ2> SEQ> CCNCGTTTTAGTAATTAATA ALN-SEQ> CCNCGTTTTAGT ALN-PR> ----GTTTTAGT PRIMER> GTTTTAGT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ3> SEQ> GGGCGTTTTAGTAATTAATA ALN-SEQ> GGGCGTTTTAGT ALN-PR> ----GTTTTAGT PRIMER> GTTTTAGT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTTACT ALN-PR> ----GTTTTACT PRIMER> GTTTTACT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNNACT ALN-PR> ----NNNNNACT PRIMER> NNNNNACT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNNACT ALN-PR> ----TANNNACT PRIMER> TANNNACT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> NNNNNNNNNNNN ALN-PR> ----NNNNNNNN PRIMER> NNNNNNNN START> 4 END> 12 GAPS> 0 ERROR> 0.000000 <- test_extractAlignment() 0.000 -> test_localAlignment() TEST Ns> SEQ1> SEQ> CCACGTTTTAGTAATTAATA ALN-SEQ> CCACGTTTTAGTAATTAATA ALN-PR> -CACGTTTT----------- PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ2> SEQ> CCNCGTTTTAGTAATTAATA ALN-SEQ> CCNCGTTTTAGTAATTAATA ALN-PR> -CACGTTTT----------- PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.125000 ok test_maskSeq (tests.test_MaskPrimers.TestMaskPrimers.test_maskSeq) ... ok test_scoreAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_scoreAlignment) ... ok test_calculateSetError (tests.test_Sequence.TestSequence.test_calculateSetError) ... ok test_filterQuality (tests.test_Sequence.TestSequence.test_filterQuality) ... ok test_meanQuality (tests.test_Sequence.TestSequence.test_meanQuality) ... ok test_scoreDNA (tests.test_Sequence.TestSequence.test_scoreDNA) ... ok test_scoreSeqPair (tests.test_Sequence.TestSequence.test_scoreSeqPair) ... SEQ3> SEQ> GGGCGTTTTAGTAATTAATA ALN-SEQ> GGGCGTTTTAGTAATTAATA ALN-PR> -GGCGTTTT----------- PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTTACTAATTAATA ALN-PR> GGC-GTTTT----------- PRIMER> PR2 START> 0 END> 9 GAPS> 1 ERROR> 0.250000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNNACTAATTAATA ALN-PR> ------------ANATAA-- PRIMER> PR3 START> 12 END> 18 GAPS> 0 ERROR> 0.375000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNNACTAATTAATA ALN-PR> -GGANA-------------- PRIMER> PR3 START> 1 END> 6 GAPS> 0 ERROR> 0.375000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> None ALN-PR> None PRIMER> None START> None END> None GAPS> 0 ERROR> 1.000000 TEST INDELS> SEQ1> SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG ALN-SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG ALN-PR> ---------------ATACGTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 15 END> 38 GAPS> 0 ERROR> 0.083333 SEQ2> SEQ> CGGATCTTCTACTCAAAACCGTCCTCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG ALN-SEQ> CGGATCTTCTACTCAAAACCGTCC-TCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG ALN-PR> --------------AATAC-GTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 14 END> 38 GAPS> 2 ERROR> 0.208333 SEQ3> SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTGATCTGTTTTACATGGGGGCATCACCCAG ALN-SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTG-ATCTGTTTTACATGGGGGCATCACCCAG ALN-PR> ---------------AATACGTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 15 END> 38 GAPS> 1 ERROR> 0.125000 SEQ4> SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT ALN-SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT ALN-PR> ------CATCT-TCCTCTA------------------------------------------- PRIMER> PR2 START> 6 END> 19 GAPS> 1 ERROR> 0.250000 SEQ5> SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG ALN-SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG ALN-PR> ------CATCTTCCTCTA-------------------------------------------- PRIMER> PR2 START> 6 END> 18 GAPS> 0 ERROR> 0.166667 SEQ6> SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA ALN-SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA ALN-PR> TCT-TCCTCTA--------------------------------------------------- PRIMER> PR2 START> 0 END> 11 GAPS> 1 ERROR> 0.250000 SEQ7> SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> --GTGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 2 END> 15 GAPS> 1 ERROR> 0.083333 SEQ8> SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 3 END> 15 GAPS> 1 ERROR> 0.166667 SEQ9> SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 3 END> 15 GAPS> 1 ERROR> 0.333333 SEQ10> SEQ> -------------------------------------------------------------- ALN-SEQ> None ALN-PR> None PRIMER> None START> None END> None GAPS> 0 ERROR> 1.000000 <- test_localAlignment() 0.065 -> test_maskSeq() TEST CUT> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> AGTAATTAATA TEST MASK> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> NNNNNNAGTAATTAATA TEST TRIM> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> CGTTTTAGTAATTAATA TEST TAG> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> CCACGTTTTAGTAATTAATA <- test_maskSeq() 0.001 -> test_scoreAlignment() SEQ1> SEQ> CCACGTTTTAGTAATTAATA ALN-SEQ> CCACGTTTT ALN-PR> -CACGTTTT PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ2> SEQ> CCNCGTTTTAGTAATTAATA ALN-SEQ> CCNCGTTTT ALN-PR> -CACGTTTT PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.125000 SEQ3> SEQ> GGGCGTTTTAGTAATTAATA ALN-SEQ> GGGCGTTTT ALN-PR> -GGCGTTTT PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTT ALN-PR> -GGCGTTTT PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.250000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNN ALN-PR> -GGCGTTTT PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.750000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNN ALN-PR> -GGANATAA PRIMER> PR3 START> 1 END> 9 GAPS> 0 ERROR> 0.375000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> NNNNNNNNN ALN-PR> -CACGTTTT PRIMER> None START> 1 END> 9 GAPS> 0 ERROR> 1.000000 <- test_scoreAlignment() 0.011 -> test_calculateSetError() REF> CGGCGTAA 0.4347826086956522 REF> NNNNNNNN 1.0 <- test_calculateSetError() 0.000 -> test_filterQuality() RESULT> True 25 RESULT> False 5 RESULT> False 0 <- test_filterQuality() 0.000 -> test_meanQuality() RESULT> 25 [30, 30, 20, 20, 30, 30, 40, 40] RESULT> 5 [30, 30, 0, 0, 30, 30, 20, 20] RESULT> 0 [0, 0, 0, 0, 0, 0, 0, 0] <- test_meanQuality() 0.000 -> test_scoreDNA() Default DNA Scores> A==A> 1 A==T> 0 A==R> 1 U==T> 1 A==N> 1 N==A> 1 A==-> 0 -==A> 0 Symmetric DNA Scores> A==A> 1 A==T> 0 A==R> 1 U==T> 1 A==N> 1 N==A> 1 A==-> 1 -==A> 1 Asymmetric DNA Scores> A==A> 1 A==T> 0 A==R> 1 U==T> 1 A==N> 1 N==A> 0 A==-> 1 -==A> 0 <- test_scoreDNA() 0.000 -> test_scoreSeqPair() Default DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ6> NNNNNNAA SEQ7> --------ok test_weightDNA (tests.test_Sequence.TestSequence.test_weightDNA) ... ok test_consensusUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_consensusUnify) ... ok test_deletionUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_deletionUnify) ... ok ---------------------------------------------------------------------- Ran 40 tests in 0.300s OK (skipped=6) SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ7> -------- SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 Asymmetric DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 3 WEIGHT> 8 ERROR> 0.625000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ7> -------- SEQ8> CG------ SCORE> 0 WEIGHT> 8 ERROR> 1.000000 Masked DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 5 WEIGHT> 6 ERROR> 0.166667 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 3 WEIGHT> 6 ERROR> 0.500000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 2 WEIGHT> 2 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 3 WEIGHT> 6 ERROR> 0.500000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 4 WEIGHT> 6 ERROR> 0.333333 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 1 WEIGHT> 2 ERROR> 0.500000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 0 WEIGHT> 6 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 2 WEIGHT> 6 ERROR> 0.666667 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 6 ERROR> 0.166667 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 2 WEIGHT> 2 ERROR> 0.000000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 1 WEIGHT> 2 ERROR> 0.500000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 2 WEIGHT> 6 ERROR> 0.666667 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 6 ERROR> 0.333333 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ7> -------- SCORE> 0 WEIGHT> 2 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 0 WEIGHT> 2 ERROR> 1.000000 SEQ7> -------- SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 <- test_scoreSeqPair() 0.006 -> test_weightDNA() DNA Weight> SEQ1> 8 SEQ2> 6 SEQ3> 8 SEQ4> 6 SEQ5> 0 SEQ6> 2 SEQ7> 8 SEQ8> 8 AA Weight> SEQ1> 8 SEQ2> 6 SEQ3> 8 SEQ4> 6 <- test_weightDNA() 0.000 -> test_consensusUnify() ID> SEQ0|BARCODE=AAAA|SAMPLE=S1 -> SEQ0|BARCODE=AAAA|SAMPLE=S1 ID> SEQ1|BARCODE=AAAA|SAMPLE=S1 -> SEQ1|BARCODE=AAAA|SAMPLE=S1 ID> SEQ2|BARCODE=AAAA|SAMPLE=S2 -> SEQ2|BARCODE=AAAA|SAMPLE=S1 ID> SEQ3|BARCODE=AAAA|SAMPLE=S3 -> SEQ3|BARCODE=AAAA|SAMPLE=S1 ID> SEQ4|BARCODE=CCCC|SAMPLE=S1 -> SEQ4|BARCODE=CCCC|SAMPLE=S1 ID> SEQ5|BARCODE=CCCC|SAMPLE=S2 -> SEQ5|BARCODE=CCCC|SAMPLE=S1 ID> SEQ6|BARCODE=GGGG|SAMPLE=S2 -> SEQ6|BARCODE=GGGG|SAMPLE=S2 ID> SEQ7|BARCODE=GGGG|SAMPLE=S2 -> SEQ7|BARCODE=GGGG|SAMPLE=S2 <- test_consensusUnify() 0.000 -> test_deletionUnify() ID> SEQ0|BARCODE=AAAA|SAMPLE=S1 -> False ID> SEQ1|BARCODE=AAAA|SAMPLE=S1 -> False ID> SEQ2|BARCODE=AAAA|SAMPLE=S2 -> False ID> SEQ3|BARCODE=AAAA|SAMPLE=S3 -> False ID> SEQ4|BARCODE=CCCC|SAMPLE=S1 -> False ID> SEQ5|BARCODE=CCCC|SAMPLE=S2 -> False ID> SEQ6|BARCODE=GGGG|SAMPLE=S2 -> True ID> SEQ7|BARCODE=GGGG|SAMPLE=S2 -> True <- test_deletionUnify() 0.000 I: pybuild pybuild:308: cp -r /build/reproducible-path/presto-0.7.2/bin /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build; I: pybuild base:311: cd /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build; python3.12 -m unittest discover -v /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:293: SyntaxWarning: invalid escape sequence '\s' sub_regex = '[%s\s]+' % re.escape(''.join(delimiter)) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:368: SyntaxWarning: invalid escape sequence '\s' sub_regex = '[%s\s]+' % re.escape(''.join(delimiter[1:])) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:491: SyntaxWarning: invalid escape sequence '\s' header['SPECIES'] = re.sub('\s', '_', fields[2]) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:493: SyntaxWarning: invalid escape sequence '\(' header['FUNCTIONALITY'] = re.sub('[\(\)\[\]]', '', fields[3]) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:494: SyntaxWarning: invalid escape sequence '\s' header['PARTIAL'] = 'FALSE' if re.sub('\s', '', fields[13]) == '' else 'TRUE' /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/IO.py:34: SyntaxWarning: invalid escape sequence '\s' if replace_special: parse_id = lambda x: re.sub('[\s,=|]+', '_', x) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Applications.py:61: SyntaxWarning: invalid escape sequence '\.' version = re.sub('\.linux.*$','',version) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Applications.py:288: SyntaxWarning: invalid escape sequence '\>' id_regex = re.compile('([0-9]+\t[0-9]+nt, \>)(.+)(\.\.\.)') test_collapseAnnotation (tests.test_Annotation.TestAnnotation.test_collapseAnnotation) ... ok test_getCoordKey (tests.test_Annotation.TestAnnotation.test_getCoordKey) ... ok test_mergeAnnotation (tests.test_Annotation.TestAnnotation.test_mergeAnnotation) ... ok test_renameAnnotation (tests.test_Annotation.TestAnnotation.test_renameAnnotation) ... ok test_alignAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_alignAssembly) ... skipped '-> alignAssembly() skipped\n' test_makeBlastnDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeBlastnDb) ... skipped '-> makeBlastnDb() skipped\n' test_makeUSearchDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeUSearchDb) ... skipped '-> makeUSearchDb() skipped\n' test_referenceAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_referenceAssembly) ... skipped '-> referenceAssembly() skipped\n' test_runBlastn (tests.test_AssemblePairs.TestAssemblePairs.test_runBlastn) ... skipped '-> runBlastn() skipped\n' test_runUSearch (tests.test_AssemblePairs.TestAssemblePairs.test_runUSearch) ... skipped '-> runUSearch() skipped\n' test_calculateSetError (tests.test_BuildConsensus.TestBuildConsensus.test_calculateSetError) ... ok test_deleteSeqPositions (tests.test_BuildConsensus.TestBuildConsensus.test_deleteSeqPositions) ... ok test_findGapPositions (tests.test_BuildConsensus.TestBuildConsensus.test_findGapPositions) ... ok test_frequencyConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_frequencyConsensus) ... ok test_qualityConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_qualityConsensus) ... ok test_runCDHit (tests.test_ClusterSets.TestClusterSets.test_runCDHit) ... ok test_runUClust (tests.test_ClusterSets.TestClusterSets.test_runUClust) ... ok test_checkSeqEqual (tests.test_CollapseSeq.TestCollapseSeq.test_checkSeqEqual) ... ok test_convert454Header (tests.test_ConvertHeaders.TestConvertHeaders.test_convert454Header) ... ok test_convertGenbankHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertGenbankHeader) ... ok test_convertGenericHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertGenericHeader) ... ok test_convertIMGTHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertIMGTHeader) ... ok test_convertIlluminaHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertIlluminaHeader) ... ok test_convertSRAHeader (tests.test_ConvertHeaders.TestConvertHeaders.test_convertSRAHeader) ... ok test_calculateDistances (tests.test_EstimateError.TestEstimateError.test_calculateDistances) ... /usr/lib/python3/dist-packages/Bio/SeqRecord.py:228: BiopythonDeprecationWarning: Using a string as the sequence is deprecated and will raise a TypeError in future. It has been converted to a Seq object. warnings.warn( ok test_countMismatches (tests.test_EstimateError.TestEstimateError.test_countMismatches) ... ok test_initializeMismatchDictionary (tests.test_EstimateError.TestEstimateError.test_initializeMismatchDictionary) ... ok test_getFileType (tests.test_IO.TestIO.test_getFileType) ... ok test_extractAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_extractAlignment) ... ok test_localAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_localAlignment) ... -> test_collapseAnnotation() OrderedDict({'ID': 'SEQ1', 'TEST1': 'A', 'TEST2': 1, 'TEST3': 'First'}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'B', 'TEST2': 2, 'TEST3': 'Second'}) OrderedDict({'ID': 'SEQ1', 'TEST1': ['A', 'B'], 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'AB', 'TEST2': '12', 'TEST3': 'FirstSecond'}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '1', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '2', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B', 'TEST2': '3', 'TEST3': ['First', 'Second']}) <- test_collapseAnnotation() 0.000 -> test_getCoordKey() ['MISEQ:132:000000000-A2F3U:1:1101:14340:1555', 'HWI-EAS209_0006_FC706VJ:5:58:5894:21141', 'MS6_33112:1:1101:18371:1066'] ['SRR001666.1', 'SRR735691.1', 'SRR1383326.1', 'SRR1383326.1', 'ERR346596.6'] ['000034_0199_0169', 'GXGJ56Z01AE06X'] <- test_getCoordKey() 0.000 -> test_mergeAnnotation() OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,C,C', 'TEST2': '1,2,3', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'C,C,A,B', 'TEST2': '3,1,2', 'TEST3': ['First', 'Second']}) <- test_mergeAnnotation() 0.000 -> test_renameAnnotation() OrderedDict({'ID': 'SEQ1', 'RENAMED1': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'RENAMED2': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2,First,Second'}) <- test_renameAnnotation() 0.008 -> test_calculateSetError() Frequency consensus error> REF> CGGCGTAA SEQ1> CGGCGTAA SEQ2> CCNNGTAA SEQ3> CGGC--TA SEQ4> CGNN--TA SEQ5> CGGC--AA ERROR> 0.250000 Quality consensus error> REF> CGGCNNAA SEQ1> CGGCGTAA SEQ2> CCNNGTAA SEQ3> CGGC--TA SEQ4> CGNN--TA SEQ5> CGGC--AA ERROR> 0.233333 <- test_calculateSetError() 0.000 -> test_deleteSeqPositions() MAX_GAP=0.4> CGGCAA MAX_GAP=0.8> CGGCGTAA <- test_deleteSeqPositions() 0.000 -> test_findGapPositions() MAX_GAP=0.4> [4, 5] MAX_GAP=0.8> [] <- test_findGapPositions() 0.000 -> test_frequencyConsensus() MIN_FREQ=0.2> CGGCGTAA MIN_FREQ=0.8> CGGCGTNA <- test_frequencyConsensus() 0.000 -> test_qualityConsensus() MIN_QUAL=0> CGGCGTAA [90, 90, 36, 36, 16, 16, 72, 90] MIN_QUAL=20> CGGCNNAA [90, 90, 36, 36, 0, 0, 72, 90] MIN_FREQ=0.8> CGGCNNNA [90, 90, 36, 36, 0, 0, 0, 90] <- test_qualityConsensus() 0.000 -> test_runCDHit() FULL_LENGTH> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} TRIMMED> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} ZERO_LENGTH> None <- test_runCDHit() 0.066 -> test_runUClust() FULL_LENGTH> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} TRIMMED> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} ZERO_LENGTH> None <- test_runUClust() 0.055 -> test_checkSeqEqual() DNA Equality> SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA EQUAL> True SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA SEQ3|COUNT=3> CCACGTTTTACTAATTAATA EQUAL> False SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA SEQ4|COUNT=4> CCACGTTTTANTAATTAATA EQUAL> True SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA SEQ3|COUNT=3> CCACGTTTTACTAATTAATA EQUAL> False SEQ2|COUNT=2> CCACGTTTTAGTAATTAATA SEQ4|COUNT=4> CCACGTTTTANTAATTAATA EQUAL> True SEQ3|COUNT=3> CCACGTTTTACTAATTAATA SEQ4|COUNT=4> CCACGTTTTANTAATTAATA EQUAL> True <- test_checkSeqEqual() 0.000 -> test_convert454Header() OrderedDict({'ID': '000034_0199_0169', 'LENGTH': '437', 'UACCNO': 'GNDG01201ARRCR'}) OrderedDict({'ID': 'GXGJ56Z01AE06X', 'LENGTH': '222'}) <- test_convert454Header() 0.000 -> test_convertGenbankHeader() OrderedDict({'ID': 'CM000663.2', 'GI': '568336023', 'SOURCE': 'gb', 'DESC': 'Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) OrderedDict({'ID': 'CM000663.2', 'DESC': 'Homo_sapiens_chromosome_1__GRCh38_reference_primary_assembly'}) <- test_convertGenbankHeader() 0.000 -> test_convertGenericHeader() OrderedDict({'ID': 'gi_568336023_gb_CM000663.2_Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) OrderedDict({'ID': 'CM000663.2_Homo_sapiens_chromosome_1_GRCh38_reference_primary_assembly'}) OrderedDict({'ID': 'M99641_IGHV1-18*01_Homo_sapiens_F_V-REGION_188..483_296_nt_1_296+24_320_'}) OrderedDict({'ID': "Z29978_IGHV1-69*07_Homo_sapiens_F_V-REGION_1..233_233_nt_1_233+58_291_partial_in_5'_and_in_3'_"}) OrderedDict({'ID': 'AB019439_IGHV(III)-22-2*01_Homo_sapiens_P_L-PART1+V-EXON_168065..168119+168222..168262_96_nt_1_96+0_96_'}) OrderedDict({'ID': 'AE000659_TRAV11*01_Homo_sapiens_(P)_V-REGION_85121..85397_276_nt_1_276+42_318_'}) <- test_convertGenericHeader() 0.000 -> test_convertIMGTHeader() OrderedDict({'ID': 'IGHV1-18*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'F', 'PARTIAL': 'FALSE', 'ACCESSION': 'M99641'}) OrderedDict({'ID': 'IGHV1-69*07', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'F', 'PARTIAL': 'TRUE', 'ACCESSION': 'Z29978'}) OrderedDict({'ID': 'IGHV(III)-22-2*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'L-PART1+V-EXON', 'FUNCTIONALITY': 'P', 'PARTIAL': 'FALSE', 'ACCESSION': 'AB019439'}) OrderedDict({'ID': 'TRAV11*01', 'SPECIES': 'Homo_sapiens', 'REGION': 'V-REGION', 'FUNCTIONALITY': 'P', 'PARTIAL': 'FALSE', 'ACCESSION': 'AE000659'}) OrderedDict({'ID': 'IGHV1-18*01'}) OrderedDict({'ID': 'IGHV1-69*07'}) OrderedDict({'ID': 'IGHV(III)-22-2*01'}) OrderedDict({'ID': 'TRAV11*01'}) <- test_convertIMGTHeader() 0.000 -> test_convertIlluminaHeader() OrderedDict({'ID': 'MISEQ:132:000000000-A2F3U:1:1101:14340:1555', 'INDEX': 'ATCACG', 'READ': '1'}) OrderedDict({'ID': 'HWI-EAS209_0006_FC706VJ:5:58:5894:21141', 'INDEX': 'ATCACG', 'READ': '1'}) OrderedDict({'ID': 'MS6_33112:1:1101:18371:1066', 'READ': '1'}) <- test_convertIlluminaHeader() 0.000 -> test_convertSRAHeader() OrderedDict({'ID': 'SRR001666.1', 'DESC': '071112_SLXA-EAS1_s_7:5:1:817:345', 'LENGTH': '36'}) OrderedDict({'ID': 'SRR735691.1', 'DESC': 'GXGJ56Z01AE06X', 'LENGTH': '222'}) OrderedDict({'ID': 'SRR1383326.1', 'DESC': '1', 'LENGTH': '250'}) OrderedDict({'ID': 'SRR1383326.1', 'READ': '2', 'DESC': '1', 'LENGTH': '250'}) OrderedDict({'ID': 'ERR346596.6', 'DESC': 'BS-DSFCONTROL04:4:000000000-A3F0Y:1:1101:13220:1649/1'}) <- test_convertSRAHeader() 0.000 -> test_calculateDistances() <- test_calculateDistances() 0.002 -> test_countMismatches() <- test_countMismatches() 0.001 -> test_initializeMismatchDictionary() <- test_initializeMismatchDictionary() 0.000 -> test_getFileType() <- test_getFileType() 0.000 -> test_extractAlignment() SEQ1> SEQ> CCACGTTTTAGTAATTAATA ALN-SEQ> CCACGTTTTAGT ALN-PR> ----GTTTTAGT PRIMER> GTTTTAGT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ2> SEQ> CCNCGTTTTAGTAATTAATA ALN-SEQ> CCNCGTTTTAGT ALN-PR> ----GTTTTAGT PRIMER> GTTTTAGT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ3> SEQ> GGGCGTTTTAGTAATTAATA ALN-SEQ> GGGCGTTTTAGT ALN-PR> ----GTTTTAGT PRIMER> GTTTTAGT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTTACT ALN-PR> ----GTTTTACT PRIMER> GTTTTACT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNNACT ALN-PR> ----NNNNNACT PRIMER> NNNNNACT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNNACT ALN-PR> ----TANNNACT PRIMER> TANNNACT START> 4 END> 12 GAPS> 0 ERROR> 0.000000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> NNNNNNNNNNNN ALN-PR> ----NNNNNNNN PRIMER> NNNNNNNN START> 4 END> 12 GAPS> 0 ERROR> 0.000000 <- test_extractAlignment() 0.012 -> test_localAlignment() TEST Ns> SEQ1> SEQ> CCACGTTTTAGTAATTAATA ALN-SEQ> CCACGTTTTAGTAATTAATA ALN-PR> -CACGTTTT----------- PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ2> SEQ> CCNCGTTTTAGTAATTAATA ALN-SEQ> CCNCGTTTTAGTAATTAATA ALN-PR> -CACGTTTT----------- PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.125000 ok test_maskSeq (tests.test_MaskPrimers.TestMaskPrimers.test_maskSeq) ... ok test_scoreAlignment (tests.test_MaskPrimers.TestMaskPrimers.test_scoreAlignment) ... ok test_calculateSetError (tests.test_Sequence.TestSequence.test_calculateSetError) ... ok test_filterQuality (tests.test_Sequence.TestSequence.test_filterQuality) ... ok test_meanQuality (tests.test_Sequence.TestSequence.test_meanQuality) ... ok test_scoreDNA (tests.test_Sequence.TestSequence.test_scoreDNA) ... ok test_scoreSeqPair (tests.test_Sequence.TestSequence.test_scoreSeqPair) ... SEQ3> SEQ> GGGCGTTTTAGTAATTAATA ALN-SEQ> GGGCGTTTTAGTAATTAATA ALN-PR> -GGCGTTTT----------- PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTTACTAATTAATA ALN-PR> GGC-GTTTT----------- PRIMER> PR2 START> 0 END> 9 GAPS> 1 ERROR> 0.250000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNNACTAATTAATA ALN-PR> ------------ANATAA-- PRIMER> PR3 START> 12 END> 18 GAPS> 0 ERROR> 0.375000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNNACTAATTAATA ALN-PR> -GGANA-------------- PRIMER> PR3 START> 1 END> 6 GAPS> 0 ERROR> 0.375000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> None ALN-PR> None PRIMER> None START> None END> None GAPS> 0 ERROR> 1.000000 TEST INDELS> SEQ1> SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG ALN-SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG ALN-PR> ---------------ATACGTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 15 END> 38 GAPS> 0 ERROR> 0.083333 SEQ2> SEQ> CGGATCTTCTACTCAAAACCGTCCTCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG ALN-SEQ> CGGATCTTCTACTCAAAACCGTCC-TCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG ALN-PR> --------------AATAC-GTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 14 END> 38 GAPS> 2 ERROR> 0.208333 SEQ3> SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTGATCTGTTTTACATGGGGGCATCACCCAG ALN-SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTG-ATCTGTTTTACATGGGGGCATCACCCAG ALN-PR> ---------------AATACGTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 15 END> 38 GAPS> 1 ERROR> 0.125000 SEQ4> SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT ALN-SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT ALN-PR> ------CATCT-TCCTCTA------------------------------------------- PRIMER> PR2 START> 6 END> 19 GAPS> 1 ERROR> 0.250000 SEQ5> SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG ALN-SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG ALN-PR> ------CATCTTCCTCTA-------------------------------------------- PRIMER> PR2 START> 6 END> 18 GAPS> 0 ERROR> 0.166667 SEQ6> SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA ALN-SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA ALN-PR> TCT-TCCTCTA--------------------------------------------------- PRIMER> PR2 START> 0 END> 11 GAPS> 1 ERROR> 0.250000 SEQ7> SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> --GTGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 2 END> 15 GAPS> 1 ERROR> 0.083333 SEQ8> SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 3 END> 15 GAPS> 1 ERROR> 0.166667 SEQ9> SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 3 END> 15 GAPS> 1 ERROR> 0.333333 SEQ10> SEQ> -------------------------------------------------------------- ALN-SEQ> None ALN-PR> None PRIMER> None START> None END> None GAPS> 0 ERROR> 1.000000 <- test_localAlignment() 0.081 -> test_maskSeq() TEST CUT> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> AGTAATTAATA TEST MASK> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> NNNNNNAGTAATTAATA TEST TRIM> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> CGTTTTAGTAATTAATA TEST TAG> ID> SEQ|PRIMER=A|BARCODE=CCA SEQ> CCACGTTTTAGTAATTAATA <- test_maskSeq() 0.001 -> test_scoreAlignment() SEQ1> SEQ> CCACGTTTTAGTAATTAATA ALN-SEQ> CCACGTTTT ALN-PR> -CACGTTTT PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ2> SEQ> CCNCGTTTTAGTAATTAATA ALN-SEQ> CCNCGTTTT ALN-PR> -CACGTTTT PRIMER> PR1 START> 1 END> 9 GAPS> 0 ERROR> 0.125000 SEQ3> SEQ> GGGCGTTTTAGTAATTAATA ALN-SEQ> GGGCGTTTT ALN-PR> -GGCGTTTT PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTT ALN-PR> -GGCGTTTT PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.250000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNN ALN-PR> -GGCGTTTT PRIMER> PR2 START> 1 END> 9 GAPS> 0 ERROR> 0.750000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNN ALN-PR> -GGANATAA PRIMER> PR3 START> 1 END> 9 GAPS> 0 ERROR> 0.375000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> NNNNNNNNN ALN-PR> -CACGTTTT PRIMER> None START> 1 END> 9 GAPS> 0 ERROR> 1.000000 <- test_scoreAlignment() 0.016 -> test_calculateSetError() REF> CGGCGTAA 0.4347826086956522 REF> NNNNNNNN 1.0 <- test_calculateSetError() 0.000 -> test_filterQuality() RESULT> True 25 RESULT> False 5 RESULT> False 0 <- test_filterQuality() 0.000 -> test_meanQuality() RESULT> 25 [30, 30, 20, 20, 30, 30, 40, 40] RESULT> 5 [30, 30, 0, 0, 30, 30, 20, 20] RESULT> 0 [0, 0, 0, 0, 0, 0, 0, 0] <- test_meanQuality() 0.000 -> test_scoreDNA() Default DNA Scores> A==A> 1 A==T> 0 A==R> 1 U==T> 1 A==N> 1 N==A> 1 A==-> 0 -==A> 0 Symmetric DNA Scores> A==A> 1 A==T> 0 A==R> 1 U==T> 1 A==N> 1 N==A> 1 A==-> 1 -==A> 1 Asymmetric DNA Scores> A==A> 1 A==T> 0 A==R> 1 U==T> 1 A==N> 1 N==A> 0 A==-> 1 -==A> 0 <- test_scoreDNA() 0.000 -> test_scoreSeqPair() Default DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ6> NNNNNNAA SEQ7> --------ok test_weightDNA (tests.test_Sequence.TestSequence.test_weightDNA) ... ok test_consensusUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_consensusUnify) ... ok test_deletionUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_deletionUnify) ... ok ---------------------------------------------------------------------- Ran 40 tests in 0.270s OK (skipped=6) SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ7> -------- SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 Asymmetric DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 3 WEIGHT> 8 ERROR> 0.625000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ7> -------- SEQ8> CG------ SCORE> 0 WEIGHT> 8 ERROR> 1.000000 Masked DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 5 WEIGHT> 6 ERROR> 0.166667 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 3 WEIGHT> 6 ERROR> 0.500000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 2 WEIGHT> 2 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 3 WEIGHT> 6 ERROR> 0.500000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 4 WEIGHT> 6 ERROR> 0.333333 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 1 WEIGHT> 2 ERROR> 0.500000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 0 WEIGHT> 6 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 2 WEIGHT> 6 ERROR> 0.666667 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 6 ERROR> 0.166667 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 2 WEIGHT> 2 ERROR> 0.000000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 1 WEIGHT> 2 ERROR> 0.500000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 2 WEIGHT> 6 ERROR> 0.666667 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 6 ERROR> 0.333333 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ7> -------- SCORE> 0 WEIGHT> 2 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 0 WEIGHT> 2 ERROR> 1.000000 SEQ7> -------- SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 <- test_scoreSeqPair() 0.006 -> test_weightDNA() DNA Weight> SEQ1> 8 SEQ2> 6 SEQ3> 8 SEQ4> 6 SEQ5> 0 SEQ6> 2 SEQ7> 8 SEQ8> 8 AA Weight> SEQ1> 8 SEQ2> 6 SEQ3> 8 SEQ4> 6 <- test_weightDNA() 0.000 -> test_consensusUnify() ID> SEQ0|BARCODE=AAAA|SAMPLE=S1 -> SEQ0|BARCODE=AAAA|SAMPLE=S1 ID> SEQ1|BARCODE=AAAA|SAMPLE=S1 -> SEQ1|BARCODE=AAAA|SAMPLE=S1 ID> SEQ2|BARCODE=AAAA|SAMPLE=S2 -> SEQ2|BARCODE=AAAA|SAMPLE=S1 ID> SEQ3|BARCODE=AAAA|SAMPLE=S3 -> SEQ3|BARCODE=AAAA|SAMPLE=S1 ID> SEQ4|BARCODE=CCCC|SAMPLE=S1 -> SEQ4|BARCODE=CCCC|SAMPLE=S1 ID> SEQ5|BARCODE=CCCC|SAMPLE=S2 -> SEQ5|BARCODE=CCCC|SAMPLE=S1 ID> SEQ6|BARCODE=GGGG|SAMPLE=S2 -> SEQ6|BARCODE=GGGG|SAMPLE=S2 ID> SEQ7|BARCODE=GGGG|SAMPLE=S2 -> SEQ7|BARCODE=GGGG|SAMPLE=S2 <- test_consensusUnify() 0.000 -> test_deletionUnify() ID> SEQ0|BARCODE=AAAA|SAMPLE=S1 -> False ID> SEQ1|BARCODE=AAAA|SAMPLE=S1 -> False ID> SEQ2|BARCODE=AAAA|SAMPLE=S2 -> False ID> SEQ3|BARCODE=AAAA|SAMPLE=S3 -> False ID> SEQ4|BARCODE=CCCC|SAMPLE=S1 -> False ID> SEQ5|BARCODE=CCCC|SAMPLE=S2 -> False ID> SEQ6|BARCODE=GGGG|SAMPLE=S2 -> True ID> SEQ7|BARCODE=GGGG|SAMPLE=S2 -> True <- test_deletionUnify() 0.000 create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py install --root /build/reproducible-path/presto-0.7.2/debian/python3-presto running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_scripts running install_lib creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/UnifyHeaders.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/MaskPrimers.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/EstimateError.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/ConvertHeaders.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/CollapseSeq.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/ClusterSets.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/BuildConsensus.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/__pycache__/AssemblePairs.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/UnifyHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/SplitSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/ParseLog.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/ParseHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/PairSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/MaskPrimers.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/FilterSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/EstimateError.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/ConvertHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/CollapseSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/ClusterSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/BuildConsensus.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/AssemblePairs.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/bin/AlignSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Multiprocessing.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Sequence.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Applications.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Commandline.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/IO.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Annotation.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Defaults.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/Version.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Annotation.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Applications.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Commandline.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Defaults.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/IO.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Multiprocessing.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Sequence.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/Version.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/__init__.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/UnifyHeaders.py to UnifyHeaders.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/SplitSeq.py to SplitSeq.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/ParseLog.py to ParseLog.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/ParseHeaders.py to ParseHeaders.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/PairSeq.py to PairSeq.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/MaskPrimers.py to MaskPrimers.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/FilterSeq.py to FilterSeq.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/EstimateError.py to EstimateError.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/ConvertHeaders.py to ConvertHeaders.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/CollapseSeq.py to CollapseSeq.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/ClusterSets.py to ClusterSets.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/BuildConsensus.py to BuildConsensus.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/AssemblePairs.py to AssemblePairs.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/bin/AlignSets.py to AlignSets.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Annotation.py to Annotation.cpython-313.pyc /usr/lib/python3.13/dist-packages/presto/Annotation.py:293: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.13/dist-packages/presto/Annotation.py:368: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.13/dist-packages/presto/Annotation.py:491: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.13/dist-packages/presto/Annotation.py:493: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.13/dist-packages/presto/Annotation.py:494: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Applications.py to Applications.cpython-313.pyc /usr/lib/python3.13/dist-packages/presto/Applications.py:61: SyntaxWarning: invalid escape sequence '\.' /usr/lib/python3.13/dist-packages/presto/Applications.py:288: SyntaxWarning: invalid escape sequence '\>' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Commandline.py to Commandline.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Defaults.py to Defaults.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/IO.py to IO.cpython-313.pyc /usr/lib/python3.13/dist-packages/presto/IO.py:34: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Multiprocessing.py to Multiprocessing.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Sequence.py to Sequence.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/Version.py to Version.cpython-313.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto/__init__.py to __init__.cpython-313.pyc running install_egg_info running egg_info creating presto.egg-info writing presto.egg-info/PKG-INFO writing dependency_links to presto.egg-info/dependency_links.txt writing requirements to presto.egg-info/requires.txt writing top-level names to presto.egg-info/top_level.txt writing manifest file 'presto.egg-info/SOURCES.txt' reading manifest file 'presto.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'presto.egg-info/SOURCES.txt' Copying presto.egg-info to /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto-0.7.2.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/UnifyHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/SplitSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/ParseLog.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/ParseHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/PairSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/MaskPrimers.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/FilterSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/EstimateError.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/ConvertHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/CollapseSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/ClusterSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/BuildConsensus.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/AssemblePairs.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.13/AlignSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/UnifyHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/SplitSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ParseLog.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ParseHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/PairSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/MaskPrimers.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/FilterSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/EstimateError.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ConvertHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/CollapseSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ClusterSets.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/BuildConsensus.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/AssemblePairs.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/AlignSets.py to 755 I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/presto-0.7.2/debian/python3-presto running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_scripts running install_lib creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/UnifyHeaders.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/MaskPrimers.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/EstimateError.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/ConvertHeaders.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/CollapseSeq.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/ClusterSets.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/BuildConsensus.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/AssemblePairs.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/UnifyHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/SplitSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/ParseLog.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/ParseHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/PairSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/MaskPrimers.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/FilterSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/EstimateError.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/ConvertHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/CollapseSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/ClusterSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/BuildConsensus.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/AssemblePairs.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/AlignSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Multiprocessing.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Sequence.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Applications.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Commandline.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/IO.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Annotation.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Defaults.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/Version.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Applications.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Commandline.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Defaults.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/IO.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Multiprocessing.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Sequence.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Version.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/__init__.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/UnifyHeaders.py to UnifyHeaders.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/SplitSeq.py to SplitSeq.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/ParseLog.py to ParseLog.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/ParseHeaders.py to ParseHeaders.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/PairSeq.py to PairSeq.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/MaskPrimers.py to MaskPrimers.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/FilterSeq.py to FilterSeq.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/EstimateError.py to EstimateError.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/ConvertHeaders.py to ConvertHeaders.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/CollapseSeq.py to CollapseSeq.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/ClusterSets.py to ClusterSets.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/BuildConsensus.py to BuildConsensus.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/AssemblePairs.py to AssemblePairs.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/AlignSets.py to AlignSets.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Annotation.py to Annotation.cpython-312.pyc /usr/lib/python3.12/dist-packages/presto/Annotation.py:293: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/presto/Annotation.py:368: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/presto/Annotation.py:491: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/presto/Annotation.py:493: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/presto/Annotation.py:494: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Applications.py to Applications.cpython-312.pyc /usr/lib/python3.12/dist-packages/presto/Applications.py:61: SyntaxWarning: invalid escape sequence '\.' /usr/lib/python3.12/dist-packages/presto/Applications.py:288: SyntaxWarning: invalid escape sequence '\>' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Commandline.py to Commandline.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Defaults.py to Defaults.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/IO.py to IO.cpython-312.pyc /usr/lib/python3.12/dist-packages/presto/IO.py:34: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Multiprocessing.py to Multiprocessing.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Sequence.py to Sequence.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Version.py to Version.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/__init__.py to __init__.cpython-312.pyc running install_egg_info running egg_info writing presto.egg-info/PKG-INFO writing dependency_links to presto.egg-info/dependency_links.txt writing requirements to presto.egg-info/requires.txt writing top-level names to presto.egg-info/top_level.txt reading manifest file 'presto.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'presto.egg-info/SOURCES.txt' Copying presto.egg-info to /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto-0.7.2.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.12/UnifyHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/SplitSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/ParseLog.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/ParseHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/PairSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/MaskPrimers.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/FilterSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/EstimateError.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/ConvertHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/CollapseSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/ClusterSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/BuildConsensus.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/AssemblePairs.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/AlignSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/UnifyHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/SplitSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ParseLog.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ParseHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/PairSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/MaskPrimers.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/FilterSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/EstimateError.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ConvertHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/CollapseSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ClusterSets.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/BuildConsensus.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/AssemblePairs.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/AlignSets.py to 755 debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/presto-0.7.2' dh_install mkdir -p debian/presto/usr mv debian/python3-presto/usr/bin debian/presto/usr make[1]: Leaving directory '/build/reproducible-path/presto-0.7.2' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/presto-0.7.2' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/presto-0.7.2' dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-presto' in '../python3-presto_0.7.2-1_arm64.deb'. dpkg-deb: building package 'presto' in '../presto_0.7.2-1_all.deb'. dpkg-genbuildinfo --build=binary -O../presto_0.7.2-1_arm64.buildinfo dpkg-genchanges --build=binary -O../presto_0.7.2-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from presto-0.7.2/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1028729/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1028729/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1028729 and its subdirectories I: Current time: Fri Nov 22 07:54:28 +14 2024 I: pbuilder-time-stamp: 1732211668 + false + set +x Thu Nov 21 17:54:28 UTC 2024 I: Signing ./b2/presto_0.7.2-1_arm64.buildinfo as presto_0.7.2-1_arm64.buildinfo.asc Thu Nov 21 17:54:28 UTC 2024 I: Signed ./b2/presto_0.7.2-1_arm64.buildinfo as ./b2/presto_0.7.2-1_arm64.buildinfo.asc Thu Nov 21 17:54:28 UTC 2024 - build #2 for presto/unstable/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Thu Nov 21 17:54:28 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-QhWHI0V6, removing. /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q: total 176 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 17:48 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 17:54 b2 -rw-r--r-- 1 jenkins jenkins 2233 Feb 19 2024 presto_0.7.2-1.dsc -rw------- 1 jenkins jenkins 160902 Nov 21 17:48 rbuildlog.AFlOsFD /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/b1: total 900 -rw-r--r-- 1 jenkins jenkins 157265 Nov 21 17:48 build.log -rw-r--r-- 1 jenkins jenkins 20772 Nov 21 17:48 presto_0.7.2-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2233 Nov 21 17:48 presto_0.7.2-1.dsc -rw-r--r-- 1 jenkins jenkins 239480 Nov 21 17:48 presto_0.7.2-1_all.deb -rw-r--r-- 1 jenkins jenkins 8117 Nov 21 17:48 presto_0.7.2-1_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8999 Nov 21 17:48 presto_0.7.2-1_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2098 Nov 21 17:48 presto_0.7.2-1_arm64.changes -rw-r--r-- 1 jenkins jenkins 2135 Nov 21 17:48 presto_0.7.2-1_source.changes -rw-r--r-- 1 jenkins jenkins 361536 Nov 21 17:48 presto_0.7.2.orig.tar.xz -rw-r--r-- 1 jenkins jenkins 79604 Nov 21 17:48 python3-presto_0.7.2-1_arm64.deb /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/b2: total 884 -rw-r--r-- 1 jenkins jenkins 159211 Nov 21 17:54 build.log -rw-r--r-- 1 jenkins jenkins 20772 Nov 21 17:54 presto_0.7.2-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2233 Nov 21 17:54 presto_0.7.2-1.dsc -rw-r--r-- 1 jenkins jenkins 239480 Nov 21 17:54 presto_0.7.2-1_all.deb -rw-r--r-- 1 jenkins jenkins 8117 Nov 21 17:54 presto_0.7.2-1_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8999 Nov 21 17:54 presto_0.7.2-1_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2098 Nov 21 17:54 presto_0.7.2-1_arm64.changes -rw-r--r-- 1 jenkins jenkins 2135 Nov 21 17:54 presto_0.7.2-1_source.changes -rw-r--r-- 1 jenkins jenkins 361536 Nov 21 17:54 presto_0.7.2.orig.tar.xz -rw-r--r-- 1 jenkins jenkins 79604 Nov 21 17:54 python3-presto_0.7.2-1_arm64.deb Thu Nov 21 17:54:30 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Thu Nov 21 17:54:30 UTC 2024 I: presto_0.7.2-1_arm64.changes: Format: 1.8 Date: Mon, 19 Feb 2024 19:34:26 +0700 Source: presto Binary: presto python3-presto Architecture: all arm64 Version: 0.7.2-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Lance Lin Description: presto - toolkit for processing B and T cell sequences python3-presto - toolkit for processing B and T cell sequences (Python3 module) Changes: presto (0.7.2-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version: 4.6.2 (routine-update) * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) * d/presto.lintian-overrides: Update lintian override format on lines 3-16 * d/presto.examples: Install examples folder * d/control: Add to Depends and Build-Depends and replace testsuite with autopkgtest-pkg-pybuild to run upstream tests * d/control: Switch Architecture from all to any for python3-presto due to 'vsearch' (architecture specific dependency for ClusterSets) * d/rules: Copy bin dir to build dir for testing and remove overrides for dh_auto_clean and dh_installchangelogs * d/rules: Remove test file for architecture specific dependency (vsearch) Checksums-Sha1: ac69b16cc0f242a79a8cb82c4020432e188b6d5c 239480 presto_0.7.2-1_all.deb 30f5d4f23004d2be34c6314fa1155ea79095b3f8 8117 presto_0.7.2-1_arm64.buildinfo 10d9b04694f7a4748b74e2b6423bdb7f3421d6e2 79604 python3-presto_0.7.2-1_arm64.deb Checksums-Sha256: 153e501919d7879843ec28b9e052801ab79c49e0220e3182d6e81cb823712e7d 239480 presto_0.7.2-1_all.deb 0a9f0b681f9a0919df57802da034b09a3540fc414c798cb03a72e4c0b51ddae6 8117 presto_0.7.2-1_arm64.buildinfo f743db3f8aa8bbe433e1b003e9ceb52838b7a14fd705fbcc007ba353a5576a16 79604 python3-presto_0.7.2-1_arm64.deb Files: a5bceb56122d912e414313e07b56bc69 239480 python optional presto_0.7.2-1_all.deb a21ef2e1e6200f5f1569f83e71ac3f01 8117 python optional presto_0.7.2-1_arm64.buildinfo cc10dd8cec1cf6c7d52ef6ab1cf23f89 79604 python optional python3-presto_0.7.2-1_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/presto_0.7.2-1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/presto_0.7.2-1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/presto_0.7.2-1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/presto_0.7.2-1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/presto_0.7.2-1_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/presto_0.7.2-1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-11-21 17:48:58.417392113 +0000 +++ b2/build.log 2024-11-21 17:54:29.886436550 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Dec 24 12:10:00 -12 2025 -I: pbuilder-time-stamp: 1766621400 +I: Current time: Fri Nov 22 07:49:01 +14 2024 +I: pbuilder-time-stamp: 1732211341 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: unpacking presto_0.7.2-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2142681/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1028729/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 21 17:49 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1028729/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1028729/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='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='c8405f1704b34847bbfdcd5153f53e9f' - 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='2142681' - PS1='# ' - PS2='> ' + INVOCATION_ID=e1fddef8a19c4e94b993c20ab9ab36e8 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1028729 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.aBgKXB6Q/pbuilderrc_HOcn --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.aBgKXB6Q/b1 --logfile b1/build.log presto_0.7.2-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/pbuilderrc_N9g3 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/b2 --logfile b2/build.log presto_0.7.2-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink01-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2142681/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1028729/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -256,7 +288,7 @@ Get: 130 http://deb.debian.org/debian unstable/main arm64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 python3-scipy arm64 1.13.1-6 [18.2 MB] Get: 132 http://deb.debian.org/debian unstable/main arm64 vsearch arm64 2.29.1-1 [410 kB] -Fetched 91.9 MB in 1s (172 MB/s) +Fetched 91.9 MB in 1s (65.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (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 ... 20084 files and directories currently installed.) @@ -704,8 +736,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Dec 25 00:10:27 UTC 2025. -Universal Time is now: Thu Dec 25 00:10:27 UTC 2025. +Local time is now: Thu Nov 21 17:50:18 UTC 2024. +Universal Time is now: Thu Nov 21 17:50:18 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... @@ -819,7 +851,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/presto-0.7.2/ && 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 > ../presto_0.7.2-1_source.changes +I: user script /srv/workspace/pbuilder/1028729/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1028729/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/presto-0.7.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../presto_0.7.2-1_source.changes dpkg-buildpackage: info: source package presto dpkg-buildpackage: info: source version 0.7.2-1 dpkg-buildpackage: info: source distribution unstable @@ -1054,7 +1090,7 @@ {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} ZERO_LENGTH> None -<- test_runCDHit() 0.029 +<- test_runCDHit() 0.068 -> test_runUClust() FULL_LENGTH> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} @@ -1062,7 +1098,7 @@ {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} ZERO_LENGTH> None -<- test_runUClust() 0.025 +<- test_runUClust() 0.086 -> test_checkSeqEqual() DNA Equality> SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA @@ -1129,7 +1165,7 @@ OrderedDict({'ID': 'ERR346596.6', 'DESC': 'BS-DSFCONTROL04:4:000000000-A3F0Y:1:1101:13220:1649/1'}) <- test_convertSRAHeader() 0.000 -> test_calculateDistances() -<- test_calculateDistances() 0.002 +<- test_calculateDistances() 0.001 -> test_countMismatches() <- test_countMismatches() 0.001 -> test_initializeMismatchDictionary() @@ -1388,7 +1424,7 @@ GAPS> 0 ERROR> 1.000000 -<- test_localAlignment() 0.028 +<- test_localAlignment() 0.065 -> test_maskSeq() TEST CUT> ID> SEQ|PRIMER=A|BARCODE=CCA @@ -1478,7 +1514,7 @@ GAPS> 0 ERROR> 1.000000 -<- test_scoreAlignment() 0.007 +<- test_scoreAlignment() 0.011 -> test_calculateSetError() REF> CGGCGTAA 0.4347826086956522 REF> NNNNNNNN 1.0 @@ -1681,7 +1717,7 @@ test_deletionUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_deletionUnify) ... ok ---------------------------------------------------------------------- -Ran 40 tests in 0.110s +Ran 40 tests in 0.300s OK (skipped=6) @@ -2148,7 +2184,7 @@ OrderedDict({'ID': 'SEQ1', 'RENAMED2': 'A,B', 'TEST2': [1, 2], 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2', 'TEST3': ['First', 'Second']}) OrderedDict({'ID': 'SEQ1', 'TEST1': 'A,B,1,2,First,Second'}) -<- test_renameAnnotation() 0.000 +<- test_renameAnnotation() 0.008 -> test_calculateSetError() Frequency consensus error> REF> CGGCGTAA @@ -2191,7 +2227,7 @@ {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} ZERO_LENGTH> None -<- test_runCDHit() 0.016 +<- test_runCDHit() 0.066 -> test_runUClust() FULL_LENGTH> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} @@ -2199,7 +2235,7 @@ {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} ZERO_LENGTH> None -<- test_runUClust() 0.027 +<- test_runUClust() 0.055 -> test_checkSeqEqual() DNA Equality> SEQ1|COUNT=1> CCACGTTTTAGTAATTAATA @@ -2266,7 +2302,7 @@ OrderedDict({'ID': 'ERR346596.6', 'DESC': 'BS-DSFCONTROL04:4:000000000-A3F0Y:1:1101:13220:1649/1'}) <- test_convertSRAHeader() 0.000 -> test_calculateDistances() -<- test_calculateDistances() 0.001 +<- test_calculateDistances() 0.002 -> test_countMismatches() <- test_countMismatches() 0.001 -> test_initializeMismatchDictionary() @@ -2344,7 +2380,7 @@ GAPS> 0 ERROR> 0.000000 -<- test_extractAlignment() 0.000 +<- test_extractAlignment() 0.012 -> test_localAlignment() TEST Ns> SEQ1> @@ -2525,7 +2561,7 @@ GAPS> 0 ERROR> 1.000000 -<- test_localAlignment() 0.024 +<- test_localAlignment() 0.081 -> test_maskSeq() TEST CUT> ID> SEQ|PRIMER=A|BARCODE=CCA @@ -2615,7 +2651,7 @@ GAPS> 0 ERROR> 1.000000 -<- test_scoreAlignment() 0.007 +<- test_scoreAlignment() 0.016 -> test_calculateSetError() REF> CGGCGTAA 0.4347826086956522 REF> NNNNNNNN 1.0 @@ -2818,7 +2854,7 @@ test_deletionUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_deletionUnify) ... ok ---------------------------------------------------------------------- -Ran 40 tests in 0.097s +Ran 40 tests in 0.270s OK (skipped=6) @@ -3532,12 +3568,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1028729/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1028729/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/2142681 and its subdirectories -I: Current time: Wed Dec 24 12:11:57 -12 2025 -I: pbuilder-time-stamp: 1766621517 +I: removing directory /srv/workspace/pbuilder/1028729 and its subdirectories +I: Current time: Fri Nov 22 07:54:28 +14 2024 +I: pbuilder-time-stamp: 1732211668 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/presto_0.7.2-1.diff: 68.9% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/presto_0.7.2-1.diff.gz b2/build.log: 88.2% -- replaced with stdout Compressing the 1st log... b1/build.log: 88.5% -- replaced with stdout Thu Nov 21 17:54:31 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_presto_unstable_arm64_1732211671 + touch /var/log/reproducible-builds/diffoscope_stamp_presto_unstable_arm64_1732211671 + RESULT=0 + systemd-run '--description=diffoscope on presto/0.7.2-1 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_15-71419 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q --run-session -c jenkins-reproducible-unstable-diffoscope-8421f7c6-54f8-4ac4-9ade-835af3ae1918 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/dbd-tmp-WDcXawe ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/presto_0.7.2-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/presto_0.7.2-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/presto_0.7.2-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/b1/presto_0.7.2-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/b2/presto_0.7.2-1_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_15-71419.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/presto_0.7.2-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/presto_0.7.2-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/presto_0.7.2-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/b1/presto_0.7.2-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.aBgKXB6Q/b2/presto_0.7.2-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.411s) 0.411s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.022s) 0.022s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 750ms CPU time consumed: 748ms _ _ __ _ __ ___ ___| |_ ___ | '_ \| '__/ _ \/ __| __/ _ \ | |_) | | | __/\__ \ || (_) | | .__/|_| \___||___/\__\___/ |_| Thu Nov 21 17:54:32 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Thu Nov 21 17:54:32 UTC 2024 I: presto from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-21 17:54:33] INFO: Starting at 2024-11-21 17:54:33.508042 [2024-11-21 17:54:33] INFO: Generating the pages of 1 package(s) [2024-11-21 17:54:33] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/presto didn't produce a buildlog, even though it has been built. [2024-11-21 17:54:33] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/presto_0.7.2-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/presto_0.7.2-1.diff.gz is missing [2024-11-21 17:54:33] INFO: Finished at 2024-11-21 17:54:33.891770, took: 0:00:00.383735 Thu Nov 21 17:54:33 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/presto.html Thu Nov 21 17:54:33 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Nov 21 17:54:33 UTC 2024 I: Submitting 12K b1/presto_0.7.2-1_arm64.buildinfo.asc https://buildinfo.debian.net/30f5d4f23004d2be34c6314fa1155ea79095b3f8/presto_0.7.2-1_all Thu Nov 21 17:54:34 UTC 2024 I: Submitting 12K b2/presto_0.7.2-1_arm64.buildinfo.asc https://buildinfo.debian.net/8263cc87b900725f495e44a9c746f1ff8227c67f/presto_0.7.2-1_all Thu Nov 21 17:54:35 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Nov 21 17:54:35 UTC 2024 I: Done submitting .buildinfo files. Thu Nov 21 17:54:35 UTC 2024 I: Removing signed presto_0.7.2-1_arm64.buildinfo.asc files: removed './b1/presto_0.7.2-1_arm64.buildinfo.asc' removed './b2/presto_0.7.2-1_arm64.buildinfo.asc' 1732211675 arm64 unstable presto Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/presto_0.7.2-1.rbuild.log: 87.0% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/presto_0.7.2-1.rbuild.log.gz [2024-11-21 17:54:35] INFO: Starting at 2024-11-21 17:54:35.816054 [2024-11-21 17:54:35] INFO: Generating the pages of 1 package(s) [2024-11-21 17:54:36] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/presto_0.7.2-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/presto_0.7.2-1.diff.gz is missing [2024-11-21 17:54:36] INFO: Finished at 2024-11-21 17:54:36.272108, took: 0:00:00.456063 All cleanup done. Thu Nov 21 17:54:36 UTC 2024 - total duration: 0h 7m 49s. Thu Nov 21 17:54:36 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-fhmzQyGh, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 7min 52.793s CPU time consumed: 7.234s