I: pbuilder: network access will be disabled during build I: Current time: Thu Dec 12 19:31:41 +14 2024 I: pbuilder-time-stamp: 1733981501 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/2858/tmp/hooks/D01_modify_environment starting debug: Running on virt64z. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Dec 12 05:31 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2858/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2858/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=4892866310a54df790160a1823341cbd LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2858 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0Jx84YK4/pbuilderrc_Q7qR --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0Jx84YK4/b2 --logfile b2/build.log presto_0.7.2-2.dsc' SUDO_GID=110 SUDO_UID=103 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-28-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 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2858/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: armhf 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, 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 ... 19680 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 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} 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, 131 newly installed, 0 to remove and 0 not upgraded. Need to get 90.2 MB of archives. After unpacking 348 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf libpython3.12-minimal armhf 3.12.8-1 [801 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf python3.12-minimal armhf 3.12.8-1 [1810 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf python3-minimal armhf 3.12.7-1 [26.8 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf tzdata all 2024b-4 [256 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.2~rc1-2 [22.9 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 12 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf libtirpc3t64 armhf 1.3.4+ds-1.3+b1 [71.3 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf libnsl2 armhf 1.3.0-3+b3 [35.0 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf libreadline8t64 armhf 8.2-5 [146 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf libpython3.12-stdlib armhf 3.12.8-1 [1823 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf python3.12 armhf 3.12.8-1 [677 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf libpython3-stdlib armhf 3.12.7-1 [9712 B] Get: 22 http://deb.debian.org/debian unstable/main armhf python3 armhf 3.12.7-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf libpython3.13-minimal armhf 3.13.1-1 [843 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf python3.13-minimal armhf 3.13.1-1 [1839 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf sgml-base all 1.31 [15.4 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-6 [1091 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-12 [83.9 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 35 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 36 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB] Get: 38 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 39 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-2 [723 kB] Get: 41 http://deb.debian.org/debian unstable/main armhf cd-hit armhf 4.8.1-4 [499 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-8 [517 kB] Get: 44 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 47 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 48 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5+b1 [9088 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 53 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 54 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 55 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB] Get: 56 http://deb.debian.org/debian unstable/main armhf python3-autocommand all 2.2.2-3 [13.6 kB] Get: 57 http://deb.debian.org/debian unstable/main armhf python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 58 http://deb.debian.org/debian unstable/main armhf python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 59 http://deb.debian.org/debian unstable/main armhf python3-typeguard all 4.4.1-1 [37.0 kB] Get: 60 http://deb.debian.org/debian unstable/main armhf python3-inflect all 7.3.1-2 [32.4 kB] Get: 61 http://deb.debian.org/debian unstable/main armhf python3-jaraco.context all 6.0.0-1 [7984 B] Get: 62 http://deb.debian.org/debian unstable/main armhf python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 63 http://deb.debian.org/debian unstable/main armhf python3-pkg-resources all 75.2.0-1 [213 kB] Get: 64 http://deb.debian.org/debian unstable/main armhf python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 65 http://deb.debian.org/debian unstable/main armhf python3-zipp all 3.21.0-1 [10.6 kB] Get: 66 http://deb.debian.org/debian unstable/main armhf python3-setuptools all 75.2.0-1 [731 kB] Get: 67 http://deb.debian.org/debian unstable/main armhf dh-python all 6.20241024 [109 kB] Get: 68 http://deb.debian.org/debian unstable/main armhf fonts-dejavu-mono all 2.37-8 [489 kB] Get: 69 http://deb.debian.org/debian unstable/main armhf fonts-dejavu-core all 2.37-8 [840 kB] Get: 70 http://deb.debian.org/debian unstable/main armhf libfontenc1 armhf 1:1.1.8-1+b1 [20.8 kB] Get: 71 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB] Get: 72 http://deb.debian.org/debian unstable/main armhf libpng16-16t64 armhf 1.6.44-3 [263 kB] Get: 73 http://deb.debian.org/debian unstable/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [385 kB] Get: 74 http://deb.debian.org/debian unstable/main armhf x11-common all 1:7.7+23.1 [216 kB] Get: 75 http://deb.debian.org/debian unstable/main armhf xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 76 http://deb.debian.org/debian unstable/main armhf xfonts-utils armhf 1:7.7+7 [84.2 kB] Get: 77 http://deb.debian.org/debian unstable/main armhf fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 78 http://deb.debian.org/debian unstable/main armhf fontconfig-config armhf 2.15.0-1.1+b1 [318 kB] Get: 79 http://deb.debian.org/debian unstable/main armhf libblas3 armhf 3.12.0-4 [111 kB] Get: 80 http://deb.debian.org/debian unstable/main armhf libfontconfig1 armhf 2.15.0-1.1+b1 [371 kB] Get: 81 http://deb.debian.org/debian unstable/main armhf libpixman-1-0 armhf 0.44.0-3 [164 kB] Get: 82 http://deb.debian.org/debian unstable/main armhf libxau6 armhf 1:1.0.11-1 [19.7 kB] Get: 83 http://deb.debian.org/debian unstable/main armhf libxdmcp6 armhf 1:1.1.5-1 [26.4 kB] Get: 84 http://deb.debian.org/debian unstable/main armhf libxcb1 armhf 1.17.0-2+b1 [140 kB] Get: 85 http://deb.debian.org/debian unstable/main armhf libx11-data all 2:1.8.10-2 [337 kB] Get: 86 http://deb.debian.org/debian unstable/main armhf libx11-6 armhf 2:1.8.10-2 [750 kB] Get: 87 http://deb.debian.org/debian unstable/main armhf libxcb-render0 armhf 1.17.0-2+b1 [114 kB] Get: 88 http://deb.debian.org/debian unstable/main armhf libxcb-shm0 armhf 1.17.0-2+b1 [105 kB] Get: 89 http://deb.debian.org/debian unstable/main armhf libxext6 armhf 2:1.3.4-1+b2 [45.2 kB] Get: 90 http://deb.debian.org/debian unstable/main armhf libxrender1 armhf 1:0.9.10-1.1+b2 [25.0 kB] Get: 91 http://deb.debian.org/debian unstable/main armhf libcairo2 armhf 1.18.2-2 [443 kB] Get: 92 http://deb.debian.org/debian unstable/main armhf libdeflate0 armhf 1.22-1 [36.3 kB] Get: 93 http://deb.debian.org/debian unstable/main armhf libfribidi0 armhf 1.0.16-1 [24.6 kB] Get: 94 http://deb.debian.org/debian unstable/main armhf libgfortran5 armhf 14.2.0-8 [263 kB] Get: 95 http://deb.debian.org/debian unstable/main armhf libglib2.0-0t64 armhf 2.82.3-2 [1327 kB] Get: 96 http://deb.debian.org/debian unstable/main armhf libgraphite2-3 armhf 1.3.14-2+b1 [63.1 kB] Get: 97 http://deb.debian.org/debian unstable/main armhf libharfbuzz0b armhf 10.1.0-1 [418 kB] Get: 98 http://deb.debian.org/debian unstable/main armhf libimagequant0 armhf 2.18.0-1+b2 [30.5 kB] Get: 99 http://deb.debian.org/debian unstable/main armhf libjbig0 armhf 2.1-6.1+b2 [27.3 kB] Get: 100 http://deb.debian.org/debian unstable/main armhf libjpeg62-turbo armhf 1:2.1.5-3+b1 [145 kB] Get: 101 http://deb.debian.org/debian unstable/main armhf liblapack3 armhf 3.12.0-4 [1828 kB] Get: 102 http://deb.debian.org/debian unstable/main armhf liblbfgsb0 armhf 3.0+dfsg.4-1+b2 [25.6 kB] Get: 103 http://deb.debian.org/debian unstable/main armhf liblcms2-2 armhf 2.16-2 [131 kB] Get: 104 http://deb.debian.org/debian unstable/main armhf liblerc4 armhf 4.0.0+ds-5 [146 kB] Get: 105 http://deb.debian.org/debian unstable/main armhf libopenjp2-7 armhf 2.5.0-2+b4 [179 kB] Get: 106 http://deb.debian.org/debian unstable/main armhf libpython3.13-stdlib armhf 3.13.1-1 [1844 kB] Get: 107 http://deb.debian.org/debian unstable/main armhf libraqm0 armhf 0.10.2-1 [11.6 kB] Get: 108 http://deb.debian.org/debian unstable/main armhf libsharpyuv0 armhf 1.4.0-0.1+b1 [111 kB] Get: 109 http://deb.debian.org/debian unstable/main armhf libwebp7 armhf 1.4.0-0.1+b1 [266 kB] Get: 110 http://deb.debian.org/debian unstable/main armhf libtiff6 armhf 4.5.1+git230720-5 [302 kB] Get: 111 http://deb.debian.org/debian unstable/main armhf libwebpdemux2 armhf 1.4.0-0.1+b1 [110 kB] Get: 112 http://deb.debian.org/debian unstable/main armhf libwebpmux3 armhf 1.4.0-0.1+b1 [120 kB] Get: 113 http://deb.debian.org/debian unstable/main armhf python3.13 armhf 3.13.1-1 [740 kB] Get: 114 http://deb.debian.org/debian unstable/main armhf python3-all armhf 3.12.7-1 [1052 B] Get: 115 http://deb.debian.org/debian unstable/main armhf python3-numpy armhf 1:1.26.4+ds-12 [3676 kB] Get: 116 http://deb.debian.org/debian unstable/main armhf python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 117 http://deb.debian.org/debian unstable/main armhf python3-pil armhf 10.4.0-1+b1 [478 kB] Get: 118 http://deb.debian.org/debian unstable/main armhf python3-cairo armhf 1.26.1-2+b1 [120 kB] Get: 119 http://deb.debian.org/debian unstable/main armhf python3-freetype all 2.5.1-1 [89.3 kB] Get: 120 http://deb.debian.org/debian unstable/main armhf python3-rlpycairo all 0.3.0-3 [9904 B] Get: 121 http://deb.debian.org/debian unstable/main armhf python3-reportlab all 4.2.5-1 [1117 kB] Get: 122 http://deb.debian.org/debian unstable/main armhf xml-core all 0.19 [20.1 kB] Get: 123 http://deb.debian.org/debian unstable/main armhf w3c-sgml-lib all 1.3-3 [273 kB] Get: 124 http://deb.debian.org/debian unstable/main armhf python3-biopython armhf 1.84+dfsg-4+b1 [1625 kB] Get: 125 http://deb.debian.org/debian unstable/main armhf python3-dateutil all 2.9.0-3 [79.3 kB] Get: 126 http://deb.debian.org/debian unstable/main armhf python3-decorator all 5.1.1-5 [15.1 kB] Get: 127 http://deb.debian.org/debian unstable/main armhf python3-packaging all 24.2-1 [55.3 kB] Get: 128 http://deb.debian.org/debian unstable/main armhf python3-tz all 2024.1-2 [30.9 kB] Get: 129 http://deb.debian.org/debian unstable/main armhf python3-pandas-lib armhf 2.2.3+dfsg-5+b1 [6440 kB] Get: 130 http://deb.debian.org/debian unstable/main armhf python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 131 http://deb.debian.org/debian unstable/main armhf python3-scipy armhf 1.14.1-3 [17.8 MB] Fetched 90.2 MB in 2s (55.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:armhf. (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 ... 19680 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.8-1_armhf.deb ... Unpacking libpython3.12-minimal:armhf (3.12.8-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.4-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-1_armhf.deb ... Unpacking python3.12-minimal (3.12.8-1) ... Setting up libpython3.12-minimal:armhf (3.12.8-1) ... Setting up libexpat1:armhf (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 ... 20000 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_armhf.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:armhf. Preparing to unpack .../04-libkrb5support0_1.21.3-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.21.3-3) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../05-libcom-err2_1.47.2~rc1-2_armhf.deb ... Unpacking libcom-err2:armhf (1.47.2~rc1-2) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../06-libk5crypto3_1.21.3-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.21.3-3) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../07-libkeyutils1_1.6.3-4_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-4) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../08-libkrb5-3_1.21.3-3_armhf.deb ... Unpacking libkrb5-3:armhf (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (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:armhf. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:armhf (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:armhf. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_armhf.deb ... Unpacking libnsl2:armhf (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:armhf. Preparing to unpack .../14-libreadline8t64_8.2-5_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:armhf (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:armhf. Preparing to unpack .../15-libpython3.12-stdlib_3.12.8-1_armhf.deb ... Unpacking libpython3.12-stdlib:armhf (3.12.8-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.8-1_armhf.deb ... Unpacking python3.12 (3.12.8-1) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (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 ... 21063 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_armhf.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package libpython3.13-minimal:armhf. Preparing to unpack .../001-libpython3.13-minimal_3.13.1-1_armhf.deb ... Unpacking libpython3.13-minimal:armhf (3.13.1-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../002-python3.13-minimal_3.13.1-1_armhf.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_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../006-libmagic1t64_1%3a5.45-3+b1_armhf.deb ... 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Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../049-libbrotli1_1.1.0-2+b6_armhf.deb ... Unpacking libbrotli1:armhf (1.1.0-2+b6) ... Selecting previously unselected package libpng16-16t64:armhf. Preparing to unpack .../050-libpng16-16t64_1.6.44-3_armhf.deb ... Unpacking libpng16-16t64:armhf (1.6.44-3) ... Selecting previously unselected package libfreetype6:armhf. Preparing to unpack .../051-libfreetype6_2.13.3+dfsg-1_armhf.deb ... Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../052-x11-common_1%3a7.7+23.1_all.deb ... Unpacking x11-common (1:7.7+23.1) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../053-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../054-xfonts-utils_1%3a7.7+7_armhf.deb ... 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Preparing to unpack .../060-libxau6_1%3a1.0.11-1_armhf.deb ... Unpacking libxau6:armhf (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:armhf. Preparing to unpack .../061-libxdmcp6_1%3a1.1.5-1_armhf.deb ... Unpacking libxdmcp6:armhf (1:1.1.5-1) ... Selecting previously unselected package libxcb1:armhf. Preparing to unpack .../062-libxcb1_1.17.0-2+b1_armhf.deb ... Unpacking libxcb1:armhf (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../063-libx11-data_2%3a1.8.10-2_all.deb ... Unpacking libx11-data (2:1.8.10-2) ... Selecting previously unselected package libx11-6:armhf. Preparing to unpack .../064-libx11-6_2%3a1.8.10-2_armhf.deb ... Unpacking libx11-6:armhf (2:1.8.10-2) ... Selecting previously unselected package libxcb-render0:armhf. Preparing to unpack .../065-libxcb-render0_1.17.0-2+b1_armhf.deb ... Unpacking libxcb-render0:armhf (1.17.0-2+b1) ... Selecting previously unselected package libxcb-shm0:armhf. 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Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../072-libgfortran5_14.2.0-8_armhf.deb ... Unpacking libgfortran5:armhf (14.2.0-8) ... Selecting previously unselected package libglib2.0-0t64:armhf. Preparing to unpack .../073-libglib2.0-0t64_2.82.3-2_armhf.deb ... Unpacking libglib2.0-0t64:armhf (2.82.3-2) ... Selecting previously unselected package libgraphite2-3:armhf. Preparing to unpack .../074-libgraphite2-3_1.3.14-2+b1_armhf.deb ... Unpacking libgraphite2-3:armhf (1.3.14-2+b1) ... Selecting previously unselected package libharfbuzz0b:armhf. Preparing to unpack .../075-libharfbuzz0b_10.1.0-1_armhf.deb ... Unpacking libharfbuzz0b:armhf (10.1.0-1) ... Selecting previously unselected package libimagequant0:armhf. Preparing to unpack .../076-libimagequant0_2.18.0-1+b2_armhf.deb ... Unpacking libimagequant0:armhf (2.18.0-1+b2) ... Selecting previously unselected package libjbig0:armhf. Preparing to unpack .../077-libjbig0_2.1-6.1+b2_armhf.deb ... Unpacking libjbig0:armhf (2.1-6.1+b2) ... Selecting previously unselected package libjpeg62-turbo:armhf. Preparing to unpack .../078-libjpeg62-turbo_1%3a2.1.5-3+b1_armhf.deb ... Unpacking libjpeg62-turbo:armhf (1:2.1.5-3+b1) ... Selecting previously unselected package liblapack3:armhf. Preparing to unpack .../079-liblapack3_3.12.0-4_armhf.deb ... Unpacking liblapack3:armhf (3.12.0-4) ... Selecting previously unselected package liblbfgsb0:armhf. Preparing to unpack .../080-liblbfgsb0_3.0+dfsg.4-1+b2_armhf.deb ... Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1+b2) ... Selecting previously unselected package liblcms2-2:armhf. Preparing to unpack .../081-liblcms2-2_2.16-2_armhf.deb ... Unpacking liblcms2-2:armhf (2.16-2) ... Selecting previously unselected package liblerc4:armhf. Preparing to unpack .../082-liblerc4_4.0.0+ds-5_armhf.deb ... Unpacking liblerc4:armhf (4.0.0+ds-5) ... Selecting previously unselected package libopenjp2-7:armhf. Preparing to unpack .../083-libopenjp2-7_2.5.0-2+b4_armhf.deb ... Unpacking libopenjp2-7:armhf (2.5.0-2+b4) ... Selecting previously unselected package libpython3.13-stdlib:armhf. Preparing to unpack .../084-libpython3.13-stdlib_3.13.1-1_armhf.deb ... Unpacking libpython3.13-stdlib:armhf (3.13.1-1) ... Selecting previously unselected package libraqm0:armhf. Preparing to unpack .../085-libraqm0_0.10.2-1_armhf.deb ... Unpacking libraqm0:armhf (0.10.2-1) ... Selecting previously unselected package libsharpyuv0:armhf. Preparing to unpack .../086-libsharpyuv0_1.4.0-0.1+b1_armhf.deb ... Unpacking libsharpyuv0:armhf (1.4.0-0.1+b1) ... Selecting previously unselected package libwebp7:armhf. Preparing to unpack .../087-libwebp7_1.4.0-0.1+b1_armhf.deb ... Unpacking libwebp7:armhf (1.4.0-0.1+b1) ... Selecting previously unselected package libtiff6:armhf. Preparing to unpack .../088-libtiff6_4.5.1+git230720-5_armhf.deb ... Unpacking libtiff6:armhf (4.5.1+git230720-5) ... Selecting previously unselected package libwebpdemux2:armhf. Preparing to unpack .../089-libwebpdemux2_1.4.0-0.1+b1_armhf.deb ... Unpacking libwebpdemux2:armhf (1.4.0-0.1+b1) ... Selecting previously unselected package libwebpmux3:armhf. Preparing to unpack .../090-libwebpmux3_1.4.0-0.1+b1_armhf.deb ... Unpacking libwebpmux3:armhf (1.4.0-0.1+b1) ... Selecting previously unselected package python3.13. Preparing to unpack .../091-python3.13_3.13.1-1_armhf.deb ... Unpacking python3.13 (3.13.1-1) ... Selecting previously unselected package python3-all. Preparing to unpack .../092-python3-all_3.12.7-1_armhf.deb ... Unpacking python3-all (3.12.7-1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../093-python3-numpy_1%3a1.26.4+ds-12_armhf.deb ... Unpacking python3-numpy (1:1.26.4+ds-12) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../094-python3-chardet_5.2.0+dfsg-1_all.deb ... Unpacking python3-chardet (5.2.0+dfsg-1) ... Selecting previously unselected package python3-pil:armhf. Preparing to unpack .../095-python3-pil_10.4.0-1+b1_armhf.deb ... Unpacking python3-pil:armhf (10.4.0-1+b1) ... Selecting previously unselected package python3-cairo. Preparing to unpack .../096-python3-cairo_1.26.1-2+b1_armhf.deb ... Unpacking python3-cairo (1.26.1-2+b1) ... Selecting previously unselected package python3-freetype. Preparing to unpack .../097-python3-freetype_2.5.1-1_all.deb ... Unpacking python3-freetype (2.5.1-1) ... Selecting previously unselected package python3-rlpycairo. Preparing to unpack .../098-python3-rlpycairo_0.3.0-3_all.deb ... Unpacking python3-rlpycairo (0.3.0-3) ... Selecting previously unselected package python3-reportlab. Preparing to unpack .../099-python3-reportlab_4.2.5-1_all.deb ... Unpacking python3-reportlab (4.2.5-1) ... Selecting previously unselected package xml-core. Preparing to unpack .../100-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package w3c-sgml-lib. Preparing to unpack .../101-w3c-sgml-lib_1.3-3_all.deb ... Unpacking w3c-sgml-lib (1.3-3) ... Selecting previously unselected package python3-biopython. Preparing to unpack .../102-python3-biopython_1.84+dfsg-4+b1_armhf.deb ... Unpacking python3-biopython (1.84+dfsg-4+b1) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../103-python3-dateutil_2.9.0-3_all.deb ... Unpacking python3-dateutil (2.9.0-3) ... Selecting previously unselected package python3-decorator. Preparing to unpack .../104-python3-decorator_5.1.1-5_all.deb ... Unpacking python3-decorator (5.1.1-5) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../105-python3-packaging_24.2-1_all.deb ... Unpacking python3-packaging (24.2-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../106-python3-tz_2024.1-2_all.deb ... Unpacking python3-tz (2024.1-2) ... Selecting previously unselected package python3-pandas-lib:armhf. Preparing to unpack .../107-python3-pandas-lib_2.2.3+dfsg-5+b1_armhf.deb ... Unpacking python3-pandas-lib:armhf (2.2.3+dfsg-5+b1) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../108-python3-pandas_2.2.3+dfsg-5_all.deb ... Unpacking python3-pandas (2.2.3+dfsg-5) ... Selecting previously unselected package python3-scipy. Preparing to unpack .../109-python3-scipy_1.14.1-3_armhf.deb ... Unpacking python3-scipy (1.14.1-3) ... Setting up cd-hit (4.8.1-4) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:armhf (1.5.8-1) ... Setting up libgraphite2-3:armhf (1.3.14-2+b1) ... Setting up liblcms2-2:armhf (2.16-2) ... Setting up libpixman-1-0:armhf (0.44.0-3) ... Setting up libsharpyuv0:armhf (1.4.0-0.1+b1) ... Setting up libxau6:armhf (1:1.0.11-1) ... Setting up libxdmcp6:armhf (1:1.1.5-1) ... Setting up libkeyutils1:armhf (1.6.3-4) ... Setting up libxcb1:armhf (1.17.0-2+b1) ... Setting up libicu72:armhf (72.1-5+b1) ... Setting up liblerc4:armhf (4.0.0+ds-5) ... Setting up bsdextrautils (2.40.2-12) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libxcb-render0:armhf (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:armhf (1.1.0-2+b6) ... Setting up libmagic1t64:armhf (1:5.45-3+b1) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libdeflate0:armhf (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libxcb-shm0:armhf (1.17.0-2+b1) ... Setting up libcom-err2:armhf (1.47.2~rc1-2) ... Setting up file (1:5.45-3+b1) ... Setting up libjbig0:armhf (2.1-6.1+b2) ... Setting up libelf1t64:armhf (0.192-4) ... Setting up libkrb5support0:armhf (1.21.3-3) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Dec 12 05:32:39 UTC 2024. Universal Time is now: Thu Dec 12 05:32:39 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython3.13-minimal:armhf (3.13.1-1) ... Setting up libfontenc1:armhf (1:1.1.8-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:armhf (2.82.3-2) ... No schema files found: doing nothing. Setting up libblas3:armhf (3.12.0-4) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libjpeg62-turbo:armhf (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:armhf (1.0.16-1) ... Setting up libimagequant0:armhf (2.18.0-1+b2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:armhf (1.6.44-3) ... Setting up autopoint (0.22.5-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:armhf (1.21.3-3) ... Setting up libgfortran5:armhf (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:armhf (1.4.0-0.1+b1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:armhf (4.5.1+git230720-5) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up libopenjp2-7:armhf (2.5.0-2+b4) ... Setting up python3.13-minimal (3.13.1-1) ... Setting up libx11-6:armhf (2:1.8.10-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:armhf (1.21.3-3) ... Setting up libwebpmux3:armhf (1.4.0-0.1+b1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:armhf (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:armhf (3.12.0-4) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up gettext (0.22.5-2) ... Setting up libxrender1:armhf (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:armhf (1.4.0-0.1+b1) ... Setting up libxext6:armhf (2:1.3.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:armhf (1.21.3-3) ... Setting up libreadline8t64:armhf (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:armhf (10.1.0-1) ... Setting up libfontconfig1:armhf (2.15.0-1.1+b1) ... Setting up libpython3.13-stdlib:armhf (3.13.1-1) ... Setting up liblbfgsb0:armhf (3.0+dfsg.4-1+b2) ... Setting up libtirpc3t64:armhf (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:armhf (1.18.2-2) ... Setting up libraqm0:armhf (0.10.2-1) ... Setting up libnsl2:armhf (1.3.0-3+b3) ... Setting up libpython3.12-stdlib:armhf (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:armhf (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:armhf (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:armhf (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: user script /srv/workspace/pbuilder/2858/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/2858/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/presto-0.7.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../presto_0.7.2-2_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 armhf 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-armv7l' 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-armv7l' 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/Version.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/IO.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Commandline.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/Applications.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto copying presto/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/Annotation.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto running build_scripts creating build/scripts-3.13 copying and adjusting bin/AlignSets.py -> build/scripts-3.13 copying and adjusting bin/AssemblePairs.py -> build/scripts-3.13 copying and adjusting bin/BuildConsensus.py -> build/scripts-3.13 copying and adjusting bin/ClusterSets.py -> build/scripts-3.13 copying and adjusting bin/CollapseSeq.py -> build/scripts-3.13 copying and adjusting bin/ConvertHeaders.py -> build/scripts-3.13 copying and adjusting bin/EstimateError.py -> build/scripts-3.13 copying and adjusting bin/FilterSeq.py -> build/scripts-3.13 copying and adjusting bin/MaskPrimers.py -> build/scripts-3.13 copying and adjusting bin/PairSeq.py -> build/scripts-3.13 copying and adjusting bin/ParseHeaders.py -> build/scripts-3.13 copying and adjusting bin/ParseLog.py -> build/scripts-3.13 copying and adjusting bin/SplitSeq.py -> build/scripts-3.13 copying and adjusting bin/UnifyHeaders.py -> build/scripts-3.13 changing mode of build/scripts-3.13/AlignSets.py from 644 to 755 changing mode of build/scripts-3.13/AssemblePairs.py from 644 to 755 changing mode of build/scripts-3.13/BuildConsensus.py from 644 to 755 changing mode of build/scripts-3.13/ClusterSets.py from 644 to 755 changing mode of build/scripts-3.13/CollapseSeq.py from 644 to 755 changing mode of build/scripts-3.13/ConvertHeaders.py from 644 to 755 changing mode of build/scripts-3.13/EstimateError.py from 644 to 755 changing mode of build/scripts-3.13/FilterSeq.py from 644 to 755 changing mode of build/scripts-3.13/MaskPrimers.py from 644 to 755 changing mode of build/scripts-3.13/PairSeq.py from 644 to 755 changing mode of build/scripts-3.13/ParseHeaders.py from 644 to 755 changing mode of build/scripts-3.13/ParseLog.py from 644 to 755 changing mode of build/scripts-3.13/SplitSeq.py from 644 to 755 changing mode of build/scripts-3.13/UnifyHeaders.py from 644 to 755 I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Version.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/IO.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Commandline.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/Applications.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto copying presto/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/Annotation.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto running build_scripts creating build/scripts-3.12 copying and adjusting bin/AlignSets.py -> build/scripts-3.12 copying and adjusting bin/AssemblePairs.py -> build/scripts-3.12 copying and adjusting bin/BuildConsensus.py -> build/scripts-3.12 copying and adjusting bin/ClusterSets.py -> build/scripts-3.12 copying and adjusting bin/CollapseSeq.py -> build/scripts-3.12 copying and adjusting bin/ConvertHeaders.py -> build/scripts-3.12 copying and adjusting bin/EstimateError.py -> build/scripts-3.12 copying and adjusting bin/FilterSeq.py -> build/scripts-3.12 copying and adjusting bin/MaskPrimers.py -> build/scripts-3.12 copying and adjusting bin/PairSeq.py -> build/scripts-3.12 copying and adjusting bin/ParseHeaders.py -> build/scripts-3.12 copying and adjusting bin/ParseLog.py -> build/scripts-3.12 copying and adjusting bin/SplitSeq.py -> build/scripts-3.12 copying and adjusting bin/UnifyHeaders.py -> build/scripts-3.12 changing mode of build/scripts-3.12/AlignSets.py from 644 to 755 changing mode of build/scripts-3.12/AssemblePairs.py from 644 to 755 changing mode of build/scripts-3.12/BuildConsensus.py from 644 to 755 changing mode of build/scripts-3.12/ClusterSets.py from 644 to 755 changing mode of build/scripts-3.12/CollapseSeq.py from 644 to 755 changing mode of build/scripts-3.12/ConvertHeaders.py from 644 to 755 changing mode of build/scripts-3.12/EstimateError.py from 644 to 755 changing mode of build/scripts-3.12/FilterSeq.py from 644 to 755 changing mode of build/scripts-3.12/MaskPrimers.py from 644 to 755 changing mode of build/scripts-3.12/PairSeq.py from 644 to 755 changing mode of build/scripts-3.12/ParseHeaders.py from 644 to 755 changing mode of build/scripts-3.12/ParseLog.py from 644 to 755 changing mode of build/scripts-3.12/SplitSeq.py from 644 to 755 changing mode of build/scripts-3.12/UnifyHeaders.py from 644 to 755 dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: cp -r /build/reproducible-path/presto-0.7.2/bin /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build; rm /build/reproducible-path/presto-0.7.2/tests/test_ClusterSets.py || echo "Test file already removed or moved"; 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_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_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() 0.003 -> 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 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 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) ... 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() 0.069 -> 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() 0.004 -> 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() 0.022 -> 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() 0.001 -> 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> -------- 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> 8ok 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 38 tests in 0.139s OK (skipped=6) 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() 0.016 -> 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() 0.001 -> 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; rm /build/reproducible-path/presto-0.7.2/tests/test_ClusterSets.py || echo "Test file already removed or moved"; rm: cannot remove '/build/reproducible-path/presto-0.7.2/tests/test_ClusterSets.py': No such file or directory Test file already removed or moved 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_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() 0.001 -> 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() 0.003 -> 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 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 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) ... 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() 0.074 -> 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() 0.004 -> 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() 0.024 -> 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() 0.001 -> 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> -------- 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> 8ok 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 38 tests in 0.149s OK (skipped=6) 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() 0.019 -> 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() 0.001 -> 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 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/AlignSets.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/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/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/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/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/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/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/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/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 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__/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__/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/__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__/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/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/AssemblePairs.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 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/IO.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.13/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.13_presto/build/presto/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/Applications.py -> /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__/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__/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__/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__/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__/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__/__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/__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__/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__/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/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/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/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/Annotation.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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/IO.py to IO.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/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/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/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/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/Annotation.py to Annotation.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/BuildConsensus.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 copying build/scripts-3.13/ClusterSets.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/PairSeq.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/ParseHeaders.py -> /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/MaskPrimers.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/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/EstimateError.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 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/AlignSets.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/ParseLog.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/FilterSeq.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/UnifyHeaders.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/SplitSeq.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/EstimateError.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/AssemblePairs.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 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/AlignSets.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/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/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/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/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/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/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/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/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 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__/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__/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__/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__/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__/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__/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/__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/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/AssemblePairs.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 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/IO.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/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/Applications.py -> /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__/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__/__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/__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__/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__/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__/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__/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__/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/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/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/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/Annotation.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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/IO.py to IO.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/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/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/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/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/Annotation.py to Annotation.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/BuildConsensus.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 copying build/scripts-3.12/ClusterSets.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/PairSeq.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/ParseHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/UnifyHeaders.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/SplitSeq.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/EstimateError.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 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/AlignSets.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/ParseLog.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/FilterSeq.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/UnifyHeaders.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/SplitSeq.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/EstimateError.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/AssemblePairs.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_armhf.deb'. dpkg-deb: building package 'presto' in '../presto_0.7.2-2_all.deb'. dpkg-genbuildinfo --build=binary -O../presto_0.7.2-2_armhf.buildinfo dpkg-genchanges --build=binary -O../presto_0.7.2-2_armhf.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: user script /srv/workspace/pbuilder/2858/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2858/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2858 and its subdirectories I: Current time: Thu Dec 12 19:35:35 +14 2024 I: pbuilder-time-stamp: 1733981735