Tue Dec 10 16:42:05 UTC 2024 I: starting to build presto/unstable/arm64 on jenkins on '2024-12-10 16:41' Tue Dec 10 16:42:05 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_5/73095/console.log Tue Dec 10 16:42:05 UTC 2024 I: Downloading source for unstable/presto=0.7.2-2 --2024-12-10 16:42:05-- http://deb.debian.org/debian/pool/main/p/presto/presto_0.7.2-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2258 (2.2K) [text/prs.lines.tag] Saving to: ‘presto_0.7.2-2.dsc’ 0K .. 100% 363M=0s 2024-12-10 16:42:05 (363 MB/s) - ‘presto_0.7.2-2.dsc’ saved [2258/2258] Tue Dec 10 16:42:05 UTC 2024 I: presto_0.7.2-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: presto Binary: python3-presto, presto Architecture: any all Version: 0.7.2-2 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Homepage: https://presto.readthedocs.io Standards-Version: 4.7.0 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 db772f99a1ec2d4c0c5410dc58bf1f15f33b8506 21812 presto_0.7.2-2.debian.tar.xz Checksums-Sha256: 2eb8874e93df323a6fdf8a6e198f7795d710493d6a94d25d650a8ce0aa22c37b 361536 presto_0.7.2.orig.tar.xz afa3486409260fc81de61677149d6986e405358bbdcc013868d836564d92f383 21812 presto_0.7.2-2.debian.tar.xz Files: c10efa18782dda0f00d1a99becd31881 361536 presto_0.7.2.orig.tar.xz 937c7d10e99dbeb4b3570a5c99ff3688 21812 presto_0.7.2-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmdXXCURHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtE9lg//UF/QW+r7NEI7rIS7XMWPS8GacJqvxBvC LShqROWrNZ53UNO+DbcqMqmICsrIZb0ktI6m8TWdLbAtXR3r7MqOXO+FsYF2kxqH nURLK/K8xlqHILp9BJAqL54qspFoffhut83/2W7UrGtRCpc28+La4tx0gNH40oyC Io3m54Yt7uTVJrfNie72nkn7Eil5F87V/a4b7yjlr/cFk0QiL1NOCjsovgS0gHnT hK3t6XTPt7P5s/WCMseHGjsxH4brwbY+VLwSaOxpDE1XFEoEP2DMI6WRh5Q6qGyY +VXgcJhQH6OgaRFy885RM3uX8xEs+9b8GRHxQQ99EU0R4AamZ6+5FEsmuCo1PO38 j8eBRX1oxg7svuMCHAx1nf2DI7IaZoaNVRMXa0GrsY7DLpDihDrHplDBIilouMXP qWxFcbL2PpQkGSBEyIzebNibhC37IRM8ZIGZ7sTDsuYVG5tcB1mKKpT+WZoihoiE pRkjLeppa7srXy+X1N6vxbTizryBc0qFugy6c6IrqxQzrR//YVx7v53t1O5HzpPi 4zNnhEpAmsLV9xSBRuJtWgpiqoATTWpoozrDOrHEgSKZ0qHNEviOtnEIoj07BcaJ Ya+oCjqF6T3cHcSOCatSyDk9EouV+dBNSMPFthXg1pXclifaHA+2yTRBDRLVOM/J FyDv1V3vscc= =dsaA -----END PGP SIGNATURE----- Tue Dec 10 16:42:05 UTC 2024 I: Checking whether the package is not for us Tue Dec 10 16:42:05 UTC 2024 I: Starting 1st build on remote node codethink03-arm64.debian.net. Tue Dec 10 16:42:05 UTC 2024 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Tue Dec 10 16:44:12 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jan 12 11:05:07 -12 2026 I: pbuilder-time-stamp: 1768259107 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_0.7.2-2.dsc] I: copying [./presto_0.7.2.orig.tar.xz] I: copying [./presto_0.7.2-2.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Dec 9 21:07:49 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./presto_0.7.2-2.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_0.7.2-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying python3.12-syntax.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3562330/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='103766efcb164e189f7196ec2301483a' 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='3562330' 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.hpKflbkk/pbuilderrc_CIPE --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.hpKflbkk/b1 --logfile b1/build.log presto_0.7.2-2.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 codethink03-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3562330/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 ... 20082 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-pooch 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 92.3 MB of archives. After unpacking 422 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.8-1 [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 3.12.8-1 [1930 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-4 [256 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 1.47.2~rc1-2 [23.7 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 3.12.8-1 [1905 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.8-1 [677 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 3.13.1-1 [850 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.1-1 [1988 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 1.23.0-6 [1130 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-12 [91.4 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 1.0.16-1 [26.5 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-9 [361 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.3-1 [1412 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 10.1.0-1 [442 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 3.13.1-1 [1912 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.2-1 [13.6 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 3.13.1-1 [740 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 1.14.1-3 [18.5 MB] Get: 132 http://deb.debian.org/debian unstable/main arm64 vsearch arm64 2.29.1-1 [410 kB] Fetched 92.3 MB in 0s (225 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 ... 20082 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.8-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.8-1) ... 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_3.12.8-1_arm64.deb ... Unpacking python3.12-minimal (3.12.8-1) ... Setting up libpython3.12-minimal:arm64 (3.12.8-1) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20402 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-4_all.deb ... Unpacking tzdata (2024b-4) ... 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_1.47.2~rc1-2_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2~rc1-2) ... 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_3.12.8-1_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.8-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.8-1_arm64.deb ... Unpacking python3.12 (3.12.8-1) ... 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 ... 21465 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_3.13.1-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.1-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../002-python3.13-minimal_3.13.1-1_arm64.deb ... Unpacking python3.13-minimal (3.13.1-1) ... 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_1.23.0-6_arm64.deb ... Unpacking groff-base (1.23.0-6) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.40.2-12_arm64.deb ... Unpacking bsdextrautils (2.40.2-12) ... 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 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 (1.47.2~rc1-2) ... 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-4) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jan 12 23:05:31 UTC 2026. Universal Time is now: Mon Jan 12 23:05:31 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython3.13-minimal:arm64 (3.13.1-1) ... Setting up libfontenc1:arm64 (1:1.1.8-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.82.3-1) ... 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 (1.0.16-1) ... 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 (14.2.0-9) ... 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 (3.13.1-1) ... 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 (1.23.0-6) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:arm64 (10.1.0-1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1+b1) ... Setting up libpython3.13-stdlib:arm64 (3.13.1-1) ... 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 (3.13.1-1) ... 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 (0.10.2-1) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up libpython3.12-stdlib:arm64 (3.12.8-1) ... Setting up python3.12 (3.12.8-1) ... 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 (1.14.1-3) ... 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 (2.40-4) ... 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_0.7.2-2_source.changes dpkg-buildpackage: info: source package presto dpkg-buildpackage: info: source version 0.7.2-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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/IO.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 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/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 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/IO.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 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/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 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 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() 0.023 -> test_runUClust() FULL_LENGTH> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} TRIMMED> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} ZERO_LENGTH> None <- test_runUClust() 0.049 -> 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() 0.002 -> 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() 0.040 -> 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() 0.002 -> 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() 0.010 -> 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 0.144s 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() 0.007 -> 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 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() 0.022 -> test_runUClust() FULL_LENGTH> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} TRIMMED> {1: ['SEQ1', 'SEQ2', 'SEQ3'], 2: ['SEQ4', 'SEQ5']} ZERO_LENGTH> None <- test_runUClust() 0.049 -> 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() 0.002 -> 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() 0.042 -> 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() 0.010 -> 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 0.145s 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() 0.007 -> 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/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/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 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/IO.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/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/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 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 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 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 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/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/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 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/IO.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/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/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 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 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 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 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_0.7.2-2_arm64.deb'. dpkg-deb: building package 'presto' in '../presto_0.7.2-2_all.deb'. dpkg-genbuildinfo --build=binary -O../presto_0.7.2-2_arm64.buildinfo dpkg-genchanges --build=binary -O../presto_0.7.2-2_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: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3562330 and its subdirectories I: Current time: Mon Jan 12 11:07:11 -12 2026 I: pbuilder-time-stamp: 1768259231 Tue Dec 10 16:44:13 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink01-arm64.debian.net. Tue Dec 10 16:44:13 UTC 2024 I: Preparing to do remote build '2' on codethink01-arm64.debian.net. Tue Dec 10 16:46:38 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. Tue Dec 10 16:46:38 UTC 2024 I: presto_0.7.2-2_arm64.changes: Format: 1.8 Date: Mon, 09 Dec 2024 20:54:04 +0100 Source: presto Binary: presto python3-presto Architecture: all arm64 Version: 0.7.2-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: presto - toolkit for processing B and T cell sequences python3-presto - toolkit for processing B and T cell sequences (Python3 module) Closes: 1085789 Changes: presto (0.7.2-2) unstable; urgency=medium . * Team upload. * Fix Python3.12 string syntax Closes: #1085789 * Standards-Version: 4.7.0 (routine-update) Checksums-Sha1: 4eba34db118f1ff107202a02635794eb6e39a76d 239504 presto_0.7.2-2_all.deb 8067e0cb1c4fdf2becbf14f13218a709c7af3c4a 8177 presto_0.7.2-2_arm64.buildinfo d02710f4bf8d0dc84fbd335fa2f68742e8290395 79656 python3-presto_0.7.2-2_arm64.deb Checksums-Sha256: d23a4f898705ace714cfab5619d8c47b2210f17c7553a1aebab44b72fc83f20c 239504 presto_0.7.2-2_all.deb 6a2daa2672b7f25e6b04f231f84022fe330bc67ee4539892fb16cc5bc1d4fe53 8177 presto_0.7.2-2_arm64.buildinfo 0da31ab651e788ef45bf2ce2b0cd5616d9b0d3675cd6b10badc68ffd1744ecda 79656 python3-presto_0.7.2-2_arm64.deb Files: 87fdcaa2817fafc9293c5bfb1627429b 239504 python optional presto_0.7.2-2_all.deb 9c4e68800e4ed82e377c9c2cc889ddd6 8177 python optional presto_0.7.2-2_arm64.buildinfo cc796c12c70739a22a02d2a9c51b9965 79656 python optional python3-presto_0.7.2-2_arm64.deb Tue Dec 10 16:46:39 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_5-73095.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.hpKflbkk/presto_0.7.2-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.hpKflbkk/presto_0.7.2-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.hpKflbkk/presto_0.7.2-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.hpKflbkk/b1/presto_0.7.2-2_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.hpKflbkk/b2/presto_0.7.2-2_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: 0.383s) 0.383s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.023s) 0.023s 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: 734ms CPU time consumed: 734ms Tue Dec 10 16:46:40 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Tue Dec 10 16:46:40 UTC 2024 I: presto from unstable built successfully and reproducibly on arm64. Tue Dec 10 16:46:42 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Dec 10 16:46:42 UTC 2024 I: Submitting 12K b1/presto_0.7.2-2_arm64.buildinfo.asc Tue Dec 10 16:46:43 UTC 2024 I: Submitting 12K b2/presto_0.7.2-2_arm64.buildinfo.asc Tue Dec 10 16:46:44 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Dec 10 16:46:44 UTC 2024 I: Done submitting .buildinfo files. Tue Dec 10 16:46:44 UTC 2024 I: Removing signed presto_0.7.2-2_arm64.buildinfo.asc files: removed './b1/presto_0.7.2-2_arm64.buildinfo.asc' removed './b2/presto_0.7.2-2_arm64.buildinfo.asc'