I: pbuilder: network access will be disabled during build I: Current time: Thu Apr 4 15:36:13 +14 2024 I: pbuilder-time-stamp: 1712194573 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [presto_0.7.2-1.dsc] I: copying [./presto_0.7.2.orig.tar.xz] I: copying [./presto_0.7.2-1.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Feb 19 12:51:18 2024 gpgv: using RSA key 4A31DB5A1EE4096C87399880903649294C33F9B7 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./presto_0.7.2-1.dsc: no acceptable signature found dpkg-source: info: extracting presto in presto-0.7.2 dpkg-source: info: unpacking presto_0.7.2.orig.tar.xz dpkg-source: info: unpacking presto_0.7.2-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/9350/tmp/hooks/D01_modify_environment starting debug: Running on virt32c. 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 Apr 4 01:36 /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/9350/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/9350/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]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.21(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=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=f6a6929ca410486c9f4a321d2e81b1e0 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=9350 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.HzYPG6ZU/pbuilderrc_p1YZ --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HzYPG6ZU/b2 --logfile b2/build.log presto_0.7.2-1.dsc' SUDO_GID=113 SUDO_UID=107 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 6.1.0-18-armmp-lpae #1 SMP Debian 6.1.76-1 (2024-02-01) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 3 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/9350/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 ... 19637 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-extra{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} libbsd0{a} libcairo2{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraqm0{a} libreadline8{a} libsharpyuv0{a} libsub-override-perl{a} libtiff6{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-biopython{a} python3-cairo{a} python3-chardet{a} python3-dateutil{a} python3-decorator{a} python3-distutils{a} python3-freetype{a} python3-lib2to3{a} python3-minimal{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-six{a} python3-tz{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-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 libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-bottleneck python3-bs4 python3-html5lib python3-jinja2 python3-lxml python3-matplotlib python3-numexpr python3-odf python3-olefile python3-openpyxl python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 119 newly installed, 0 to remove and 0 not upgraded. Need to get 91.3 MB of archives. After unpacking 335 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libpython3.11-minimal armhf 3.11.8-1 [802 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.5.0-2+b2 [80.2 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf python3.11-minimal armhf 3.11.8-1 [1707 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.11.6-1 [26.2 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf tzdata all 2024a-1 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-3 [69.1 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libreadline8 armhf 8.2-3+b1 [144 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libpython3.11-stdlib armhf 3.11.8-1 [1709 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf python3.11 armhf 3.11.8-1 [597 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.11.6-1 [9224 B] Get: 13 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.11.6-1 [26.2 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf libpython3.12-minimal armhf 3.12.2-1 [793 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf python3.12-minimal armhf 3.12.2-1 [1845 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-2+b1 [314 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libmagic1 armhf 1:5.45-2+b1 [97.9 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-2+b1 [42.2 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.39.3-6 [81.2 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-1+b2 [33.4 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.0-3 [1367 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf cd-hit armhf 4.8.1-4 [499 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 40 http://deb.debian.org/debian trixie/main armhf libelf1 armhf 0.190-1+b1 [171 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1 [101 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf python3-lib2to3 all 3.11.5-1 [77.5 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf python3-distutils all 3.11.5-1 [131 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf python3-pkg-resources all 68.1.2-2 [241 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf python3-setuptools all 68.1.2-2 [468 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf dh-python all 6.20240310 [106 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-mono all 2.37-8 [489 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-core all 2.37-8 [840 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libfontenc1 armhf 1:1.1.8-1 [20.6 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf libpng16-16 armhf 1.6.43-1 [262 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf libfreetype6 armhf 2.13.2+dfsg-1+b1 [371 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf x11-common all 1:7.7+23 [252 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf xfonts-utils armhf 1:7.7+6 [84.5 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 63 http://deb.debian.org/debian trixie/main armhf fontconfig-config armhf 2.15.0-1.1 [317 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-extra all 2.37-8 [1792 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf libblas3 armhf 3.12.0-3 [108 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf libbsd0 armhf 0.12.2-1 [127 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf libfontconfig1 armhf 2.15.0-1.1 [370 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf libpixman-1-0 armhf 0.42.2-1+b1 [476 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf libxcb1 armhf 1.15-1 [140 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf libx11-data all 2:1.8.7-1 [328 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf libx11-6 armhf 2:1.8.7-1 [735 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf libxcb-render0 armhf 1.15-1 [114 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf libxcb-shm0 armhf 1.15-1 [106 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.1 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf libcairo2 armhf 1.18.0-1+b1 [441 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf libfribidi0 armhf 1.0.13-3+b1 [69.4 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf libgfortran5 armhf 14-20240201-3 [263 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf libglib2.0-0 armhf 2.78.4-1 [1281 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf libgraphite2-3 armhf 1.3.14-2 [63.2 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf libharfbuzz0b armhf 8.3.0-2 [2155 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf libimagequant0 armhf 2.18.0-1 [30.4 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf libjbig0 armhf 2.1-6.1+b1 [27.3 kB] Get: 87 http://deb.debian.org/debian trixie/main armhf libjpeg62-turbo armhf 1:2.1.5-2+b2 [143 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf liblapack3 armhf 3.12.0-3 [1803 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf liblbfgsb0 armhf 3.0+dfsg.4-1+b1 [25.5 kB] Get: 90 http://deb.debian.org/debian trixie/main armhf liblcms2-2 armhf 2.14-2+b1 [126 kB] Get: 91 http://deb.debian.org/debian trixie/main armhf liblerc4 armhf 4.0.0+ds-4+b1 [137 kB] Get: 92 http://deb.debian.org/debian trixie/main armhf libopenjp2-7 armhf 2.5.0-2+b2 [170 kB] Get: 93 http://deb.debian.org/debian trixie/main armhf libpython3.12-stdlib armhf 3.12.2-1 [1800 kB] Get: 94 http://deb.debian.org/debian trixie/main armhf libraqm0 armhf 0.10.1-1+b1 [11.8 kB] Get: 95 http://deb.debian.org/debian trixie/main armhf libsharpyuv0 armhf 1.3.2-0.4 [105 kB] Get: 96 http://deb.debian.org/debian trixie/main armhf libwebp7 armhf 1.3.2-0.4 [261 kB] Get: 97 http://deb.debian.org/debian trixie/main armhf libtiff6 armhf 4.5.1+git230720-4 [301 kB] Get: 98 http://deb.debian.org/debian trixie/main armhf libwebpdemux2 armhf 1.3.2-0.4 [106 kB] Get: 99 http://deb.debian.org/debian trixie/main armhf libwebpmux3 armhf 1.3.2-0.4 [116 kB] Get: 100 http://deb.debian.org/debian trixie/main armhf python3.12 armhf 3.12.2-1 [653 kB] Get: 101 http://deb.debian.org/debian trixie/main armhf python3-all armhf 3.11.6-1 [1060 B] Get: 102 http://deb.debian.org/debian trixie/main armhf python3-numpy armhf 1:1.24.2-2 [4016 kB] Get: 103 http://deb.debian.org/debian trixie/main armhf python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 104 http://deb.debian.org/debian trixie/main armhf python3-pil armhf 10.2.0-1 [485 kB] Get: 105 http://deb.debian.org/debian trixie/main armhf python3-cairo armhf 1.25.1-2 [130 kB] Get: 106 http://deb.debian.org/debian trixie/main armhf python3-freetype all 2.4.0-1 [80.3 kB] Get: 107 http://deb.debian.org/debian trixie/main armhf python3-rlpycairo all 0.3.0-3 [9904 B] Get: 108 http://deb.debian.org/debian trixie/main armhf python3-reportlab all 4.1.0-1 [674 kB] Get: 109 http://deb.debian.org/debian trixie/main armhf xml-core all 0.19 [20.1 kB] Get: 110 http://deb.debian.org/debian trixie/main armhf w3c-sgml-lib all 1.3-3 [273 kB] Get: 111 http://deb.debian.org/debian trixie/main armhf python3-biopython armhf 1.81+dfsg-3 [1593 kB] Get: 112 http://deb.debian.org/debian trixie/main armhf python3-six all 1.16.0-6 [16.3 kB] Get: 113 http://deb.debian.org/debian trixie/main armhf python3-dateutil all 2.9.0-2 [79.4 kB] Get: 114 http://deb.debian.org/debian trixie/main armhf python3-decorator all 5.1.1-5 [15.1 kB] Get: 115 http://deb.debian.org/debian trixie/main armhf python3-packaging all 23.2-1 [44.8 kB] Get: 116 http://deb.debian.org/debian trixie/main armhf python3-tz all 2024.1-2 [30.9 kB] Get: 117 http://deb.debian.org/debian trixie/main armhf python3-pandas-lib armhf 2.1.4+dfsg-5 [7000 kB] Get: 118 http://deb.debian.org/debian trixie/main armhf python3-pandas all 2.1.4+dfsg-5 [3015 kB] Get: 119 http://deb.debian.org/debian trixie/main armhf python3-scipy armhf 1.11.4-6 [16.9 MB] Fetched 91.3 MB in 2s (47.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. 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Unpacking python3-pil:armhf (10.2.0-1) ... Selecting previously unselected package python3-cairo. Preparing to unpack .../092-python3-cairo_1.25.1-2_armhf.deb ... Unpacking python3-cairo (1.25.1-2) ... Selecting previously unselected package python3-freetype. Preparing to unpack .../093-python3-freetype_2.4.0-1_all.deb ... Unpacking python3-freetype (2.4.0-1) ... Selecting previously unselected package python3-rlpycairo. Preparing to unpack .../094-python3-rlpycairo_0.3.0-3_all.deb ... Unpacking python3-rlpycairo (0.3.0-3) ... Selecting previously unselected package python3-reportlab. Preparing to unpack .../095-python3-reportlab_4.1.0-1_all.deb ... Unpacking python3-reportlab (4.1.0-1) ... Selecting previously unselected package xml-core. Preparing to unpack .../096-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package w3c-sgml-lib. Preparing to unpack .../097-w3c-sgml-lib_1.3-3_all.deb ... Unpacking w3c-sgml-lib (1.3-3) ... 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Selecting previously unselected package python3-pandas-lib:armhf. Preparing to unpack .../104-python3-pandas-lib_2.1.4+dfsg-5_armhf.deb ... Unpacking python3-pandas-lib:armhf (2.1.4+dfsg-5) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../105-python3-pandas_2.1.4+dfsg-5_all.deb ... Unpacking python3-pandas (2.1.4+dfsg-5) ... Selecting previously unselected package python3-scipy. Preparing to unpack .../106-python3-scipy_1.11.4-6_armhf.deb ... Unpacking python3-scipy (1.11.4-6) ... Setting up cd-hit (4.8.1-4) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:armhf (1.5.7-1+b2) ... Setting up libgraphite2-3:armhf (1.3.14-2) ... Setting up liblcms2-2:armhf (2.14-2+b1) ... Setting up libpixman-1-0:armhf (0.42.2-1+b1) ... Setting up libsharpyuv0:armhf (1.3.2-0.4) ... Setting up libxau6:armhf (1:1.0.9-1) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up liblerc4:armhf (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:armhf (2.78.4-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:armhf (1.1.0-2+b3) ... Setting up libpython3.12-minimal:armhf (3.12.2-1) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libmagic1:armhf (1:5.45-2+b1) ... Setting up libdeflate0:armhf (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2+b1) ... Setting up libjbig0:armhf (2.1-6.1+b1) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Apr 4 01:37:17 UTC 2024. Universal Time is now: Thu Apr 4 01:37:17 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:armhf (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.12.0-3) ... 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 (1:2.1.5-2+b2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:armhf (1.0.13-3+b1) ... Setting up libimagequant0:armhf (2.18.0-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16:armhf (1.6.43-1) ... Setting up autopoint (0.21-14) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libgfortran5:armhf (14-20240201-3) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:armhf (1.3.2-0.4) ... Setting up fonts-dejavu-extra (2.37-8) ... Setting up sensible-utils (0.0.22) ... Setting up libtiff6:armhf (4.5.1+git230720-4) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libopenjp2-7:armhf (2.5.0-2+b2) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libwebpmux3:armhf (1.3.2-0.4) ... Setting up libbsd0:armhf (0.12.2-1) ... Setting up libelf1:armhf (0.190-1+b1) ... Setting up readline-common (8.2-3) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b2) ... 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 (1.13.1-1) ... Setting up python3.12-minimal (3.12.2-1) ... Setting up libxdmcp6:armhf (1:1.1.2-3) ... Setting up liblapack3:armhf (3.12.0-3) ... 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 libxcb1:armhf (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:armhf (1.15-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:armhf (1.3.2-0.4) ... Setting up libreadline8:armhf (8.2-3+b1) ... Setting up libxcb-shm0:armhf (1.15-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libfreetype6:armhf (2.13.2+dfsg-1+b1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up xml-core (0.19) ... Setting up libx11-6:armhf (2:1.8.7-1) ... Setting up libharfbuzz0b:armhf (8.3.0-2) ... Setting up libfontconfig1:armhf (2.15.0-1.1) ... Setting up liblbfgsb0:armhf (3.0+dfsg.4-1+b1) ... Setting up libpython3.12-stdlib:armhf (3.12.2-1) ... Setting up libxrender1:armhf (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:armhf (3.11.8-1) ... Setting up python3.12 (3.12.2-1) ... Setting up libxext6:armhf (2:1.3.4-1+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:armhf (1.18.0-1+b1) ... Setting up libraqm0:armhf (0.10.1-1+b1) ... Setting up libpython3-stdlib:armhf (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.6-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-freetype (2.4.0-1) ... Setting up python3-tz (2024.1-2) ... Setting up python3-six (1.16.0-6) ... Setting up python3-pil:armhf (10.2.0-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (23.2-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.11.5-1) ... python3.12: can't get files for byte-compilation Setting up python3-cairo (1.25.1-2) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-all (3.11.6-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up python3-reportlab (4.1.0-1) ... Setting up dh-python (6.20240310) ... Setting up python3-scipy (1.11.4-6) ... Setting up python3-pandas-lib:armhf (2.1.4+dfsg-5) ... Setting up python3-pandas (2.1.4+dfsg-5) ... Processing triggers for libc-bin (2.37-15) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.81+dfsg-3) ... 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/9350/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/9350/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/presto-0.7.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../presto_0.7.2-1_source.changes dpkg-buildpackage: info: source package presto dpkg-buildpackage: info: source version 0.7.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Lance Lin dpkg-source --before-build . dpkg-buildpackage: info: host architecture 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:305: 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 I: pybuild base:305: python3.11 setup.py clean running clean removing '/build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build' (and everything under it) 'build/bdist.linux-armv7l' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:305: python3.12 setup.py config running config I: pybuild base:305: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:305: /usr/bin/python3.12 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/Annotation.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/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/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 running build_scripts creating build 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 I: pybuild base:305: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto copying presto/Annotation.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto copying presto/Defaults.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto copying presto/Sequence.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto copying presto/Multiprocessing.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto copying presto/Version.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto copying presto/__init__.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto copying presto/IO.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto copying presto/Commandline.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto copying presto/Applications.py -> /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto running build_scripts creating build/scripts-3.11 copying and adjusting bin/AlignSets.py -> build/scripts-3.11 copying and adjusting bin/AssemblePairs.py -> build/scripts-3.11 copying and adjusting bin/BuildConsensus.py -> build/scripts-3.11 copying and adjusting bin/ClusterSets.py -> build/scripts-3.11 copying and adjusting bin/CollapseSeq.py -> build/scripts-3.11 copying and adjusting bin/ConvertHeaders.py -> build/scripts-3.11 copying and adjusting bin/EstimateError.py -> build/scripts-3.11 copying and adjusting bin/FilterSeq.py -> build/scripts-3.11 copying and adjusting bin/MaskPrimers.py -> build/scripts-3.11 copying and adjusting bin/PairSeq.py -> build/scripts-3.11 copying and adjusting bin/ParseHeaders.py -> build/scripts-3.11 copying and adjusting bin/ParseLog.py -> build/scripts-3.11 copying and adjusting bin/SplitSeq.py -> build/scripts-3.11 copying and adjusting bin/UnifyHeaders.py -> build/scripts-3.11 changing mode of build/scripts-3.11/AlignSets.py from 644 to 755 changing mode of build/scripts-3.11/AssemblePairs.py from 644 to 755 changing mode of build/scripts-3.11/BuildConsensus.py from 644 to 755 changing mode of build/scripts-3.11/ClusterSets.py from 644 to 755 changing mode of build/scripts-3.11/CollapseSeq.py from 644 to 755 changing mode of build/scripts-3.11/ConvertHeaders.py from 644 to 755 changing mode of build/scripts-3.11/EstimateError.py from 644 to 755 changing mode of build/scripts-3.11/FilterSeq.py from 644 to 755 changing mode of build/scripts-3.11/MaskPrimers.py from 644 to 755 changing mode of build/scripts-3.11/PairSeq.py from 644 to 755 changing mode of build/scripts-3.11/ParseHeaders.py from 644 to 755 changing mode of build/scripts-3.11/ParseLog.py from 644 to 755 changing mode of build/scripts-3.11/SplitSeq.py from 644 to 755 changing mode of build/scripts-3.11/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_3.12_presto/build; rm /build/reproducible-path/presto-0.7.2/tests/test_ClusterSets.py || echo "Test file already removed or moved"; I: pybuild base:305: cd /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build; python3.12 -m unittest discover -v /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:293: SyntaxWarning: invalid escape sequence '\s' sub_regex = '[%s\s]+' % re.escape(''.join(delimiter)) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:368: SyntaxWarning: invalid escape sequence '\s' sub_regex = '[%s\s]+' % re.escape(''.join(delimiter[1:])) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:491: SyntaxWarning: invalid escape sequence '\s' header['SPECIES'] = re.sub('\s', '_', fields[2]) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:493: SyntaxWarning: invalid escape sequence '\(' header['FUNCTIONALITY'] = re.sub('[\(\)\[\]]', '', fields[3]) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py:494: SyntaxWarning: invalid escape sequence '\s' header['PARTIAL'] = 'FALSE' if re.sub('\s', '', fields[13]) == '' else 'TRUE' /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/IO.py:34: SyntaxWarning: invalid escape sequence '\s' if replace_special: parse_id = lambda x: re.sub('[\s,=|]+', '_', x) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Applications.py:61: SyntaxWarning: invalid escape sequence '\.' version = re.sub('\.linux.*$','',version) /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Applications.py:288: SyntaxWarning: invalid escape sequence '\>' id_regex = re.compile('([0-9]+\t[0-9]+nt, \>)(.+)(\.\.\.)') test_collapseAnnotation (tests.test_Annotation.TestAnnotation.test_collapseAnnotation) ... ok test_getCoordKey (tests.test_Annotation.TestAnnotation.test_getCoordKey) ... ok test_mergeAnnotation (tests.test_Annotation.TestAnnotation.test_mergeAnnotation) ... ok test_renameAnnotation (tests.test_Annotation.TestAnnotation.test_renameAnnotation) ... ok test_alignAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_alignAssembly) ... skipped '-> alignAssembly() skipped\n' test_makeBlastnDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeBlastnDb) ... skipped '-> makeBlastnDb() skipped\n' test_makeUSearchDb (tests.test_AssemblePairs.TestAssemblePairs.test_makeUSearchDb) ... skipped '-> makeUSearchDb() skipped\n' test_referenceAssembly (tests.test_AssemblePairs.TestAssemblePairs.test_referenceAssembly) ... skipped '-> referenceAssembly() skipped\n' test_runBlastn (tests.test_AssemblePairs.TestAssemblePairs.test_runBlastn) ... skipped '-> runBlastn() skipped\n' test_runUSearch (tests.test_AssemblePairs.TestAssemblePairs.test_runUSearch) ... skipped '-> runUSearch() skipped\n' test_calculateSetError (tests.test_BuildConsensus.TestBuildConsensus.test_calculateSetError) ... ok test_deleteSeqPositions (tests.test_BuildConsensus.TestBuildConsensus.test_deleteSeqPositions) ... ok test_findGapPositions (tests.test_BuildConsensus.TestBuildConsensus.test_findGapPositions) ... ok test_frequencyConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_frequencyConsensus) ... ok test_qualityConsensus (tests.test_BuildConsensus.TestBuildConsensus.test_qualityConsensus) ... ok test_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) ... 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() 0.001 -> 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() 0.001 -> 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() 0.001 -> 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() 0.004 -> 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 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) ... ERROR> 0.250000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNNACTAATTAATA ALN-PR> ------------ANATAA-- PRIMER> PR3 START> 12 END> 18 GAPS> 0 ERROR> 0.375000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNNACTAATTAATA ALN-PR> -GGANA-------------- PRIMER> PR3 START> 1 END> 6 GAPS> 0 ERROR> 0.375000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> None ALN-PR> None PRIMER> None START> None END> None GAPS> 0 ERROR> 1.000000 TEST INDELS> SEQ1> SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG ALN-SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG ALN-PR> ---------------ATACGTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 15 END> 38 GAPS> 0 ERROR> 0.083333 SEQ2> SEQ> CGGATCTTCTACTCAAAACCGTCCTCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG ALN-SEQ> CGGATCTTCTACTCAAAACCGTCC-TCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG ALN-PR> --------------AATAC-GTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 14 END> 38 GAPS> 2 ERROR> 0.208333 SEQ3> SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTGATCTGTTTTACATGGGGGCATCACCCAG ALN-SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTG-ATCTGTTTTACATGGGGGCATCACCCAG ALN-PR> ---------------AATACGTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 15 END> 38 GAPS> 1 ERROR> 0.125000 SEQ4> SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT ALN-SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT ALN-PR> ------CATCT-TCCTCTA------------------------------------------- PRIMER> PR2 START> 6 END> 19 GAPS> 1 ERROR> 0.250000 SEQ5> SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG ALN-SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG ALN-PR> ------CATCTTCCTCTA-------------------------------------------- PRIMER> PR2 START> 6 END> 18 GAPS> 0 ERROR> 0.166667 SEQ6> SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA ALN-SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA ALN-PR> TCT-TCCTCTA--------------------------------------------------- PRIMER> PR2 START> 0 END> 11 GAPS> 1 ERROR> 0.250000 SEQ7> SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> --GTGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 2 END> 15 GAPS> 1 ERROR> 0.083333 SEQ8> SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 3 END> 15 GAPS> 1 ERROR> 0.166667 SEQ9> SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 3 END> 15 GAPS> 1 ERROR> 0.333333 SEQ10> SEQ> -------------------------------------------------------------- ALN-SEQ> None ALN-PR> None PRIMER> None START> None END> None GAPS> 0 ERROR> 1.000000 <- test_localAlignment() 0.093 -> 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() 0.005 -> 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() 0.029 -> 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 ok test_weightDNA (tests.test_Sequence.TestSequence.test_weightDNA) ... ok test_consensusUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_consensusUnify) ... ok test_deletionUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_deletionUnify) ... ok ---------------------------------------------------------------------- Ran 38 tests in 0.183s OK (skipped=6) SEQ3> CGGC--AA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 3 WEIGHT> 8 ERROR> 0.625000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ7> -------- SEQ8> CG------ SCORE> 0 WEIGHT> 8 ERROR> 1.000000 Masked DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 5 WEIGHT> 6 ERROR> 0.166667 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 3 WEIGHT> 6 ERROR> 0.500000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 2 WEIGHT> 2 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 3 WEIGHT> 6 ERROR> 0.500000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 4 WEIGHT> 6 ERROR> 0.333333 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 1 WEIGHT> 2 ERROR> 0.500000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 0 WEIGHT> 6 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 2 WEIGHT> 6 ERROR> 0.666667 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 6 ERROR> 0.166667 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 2 WEIGHT> 2 ERROR> 0.000000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 1 WEIGHT> 2 ERROR> 0.500000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 2 WEIGHT> 6 ERROR> 0.666667 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 6 ERROR> 0.333333 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ7> -------- SCORE> 0 WEIGHT> 2 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 0 WEIGHT> 2 ERROR> 1.000000 SEQ7> -------- SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 <- test_scoreSeqPair() 0.020 -> 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() 0.002 -> 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_3.11_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:305: cd /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build; python3.11 -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) ... 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() 0.001 -> 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() 0.001 -> 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() 0.001 -> 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() 0.005 -> 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() 0.001 -> 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 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) ... START> 1 END> 9 GAPS> 0 ERROR> 0.000000 SEQ4> SEQ> GGNNGTTTTACTAATTAATA ALN-SEQ> GGNNGTTTTACTAATTAATA ALN-PR> GGC-GTTTT----------- PRIMER> PR2 START> 0 END> 9 GAPS> 1 ERROR> 0.250000 SEQ5> SEQ> NNGCNNNNNACTAATTAATA ALN-SEQ> NNGCNNNNNACTAATTAATA ALN-PR> ------------ANATAA-- PRIMER> PR3 START> 12 END> 18 GAPS> 0 ERROR> 0.375000 SEQ6> SEQ> GGGATANNNACTAATTAATA ALN-SEQ> GGGATANNNACTAATTAATA ALN-PR> -GGANA-------------- PRIMER> PR3 START> 1 END> 6 GAPS> 0 ERROR> 0.375000 SEQ7> SEQ> NNNNNNNNNNNNNNNNNNNN ALN-SEQ> None ALN-PR> None PRIMER> None START> None END> None GAPS> 0 ERROR> 1.000000 TEST INDELS> SEQ1> SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG ALN-SEQ> CGGATCTTCTACTCCATACGTCCGTCAGTCGTGGATCTGATCTAGCTGCGCCTTTTTCTCAG ALN-PR> ---------------ATACGTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 15 END> 38 GAPS> 0 ERROR> 0.083333 SEQ2> SEQ> CGGATCTTCTACTCAAAACCGTCCTCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG ALN-SEQ> CGGATCTTCTACTCAAAACCGTCC-TCAGTCGTGGATCTGGTCTAGCTGGGGCTGTTTCCCTG ALN-PR> --------------AATAC-GTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 14 END> 38 GAPS> 2 ERROR> 0.208333 SEQ3> SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTGATCTGTTTTACATGGGGGCATCACCCAG ALN-SEQ> GGTTTAAGTTAAGATAATACGTCCGTCAGTCGTG-ATCTGTTTTACATGGGGGCATCACCCAG ALN-PR> ---------------AATACGTCCGTCAGTCGTGGATGT------------------------ PRIMER> PR1 START> 15 END> 38 GAPS> 1 ERROR> 0.125000 SEQ4> SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT ALN-SEQ> CAACCACATGGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCT ALN-PR> ------CATCT-TCCTCTA------------------------------------------- PRIMER> PR2 START> 6 END> 19 GAPS> 1 ERROR> 0.250000 SEQ5> SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG ALN-SEQ> CAACCACATGGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTG ALN-PR> ------CATCTTCCTCTA-------------------------------------------- PRIMER> PR2 START> 6 END> 18 GAPS> 0 ERROR> 0.166667 SEQ6> SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA ALN-SEQ> TCTGTCCTCTAGAGAATCCCCTGAGAGCTCCGTTCCTCACCATGGACTGGACCTCAACCACA ALN-PR> TCT-TCCTCTA--------------------------------------------------- PRIMER> PR2 START> 0 END> 11 GAPS> 1 ERROR> 0.250000 SEQ7> SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> AGGTGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> --GTGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 2 END> 15 GAPS> 1 ERROR> 0.083333 SEQ8> SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> A--TGAAGAAGCCTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 3 END> 15 GAPS> 1 ERROR> 0.166667 SEQ9> SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-SEQ> ANNTGAAGAAGNNTGGGGCCTCCGTGAAGGTCTCCTGCTCGGCTTCTGGATACGCCTTCACC ALN-PR> ---TGAAGA-GCCTG----------------------------------------------- PRIMER> PR3 START> 3 END> 15 GAPS> 1 ERROR> 0.333333 SEQ10> SEQ> -------------------------------------------------------------- ALN-SEQ> None ALN-PR> None PRIMER> None START> None END> None GAPS> 0 ERROR> 1.000000 <- test_localAlignment() 0.095 -> 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() 0.005 -> 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() 0.030 -> 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 ok test_weightDNA (tests.test_Sequence.TestSequence.test_weightDNA) ... ok test_consensusUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_consensusUnify) ... ok test_deletionUnify (tests.test_UnifyHeaders.TestConvertHeaders.test_deletionUnify) ... ok ---------------------------------------------------------------------- Ran 38 tests in 0.188s OK (skipped=6) ERROR> 0.750000 SEQ7> -------- SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 Asymmetric DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 7 WEIGHT> 8 ERROR> 0.125000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 8 WEIGHT> 8 ERROR> 0.000000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 8 ERROR> 0.375000 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 3 WEIGHT> 8 ERROR> 0.625000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ7> -------- SEQ8> CG------ SCORE> 0 WEIGHT> 8 ERROR> 1.000000 Masked DNA Scores> SEQ1> CGGCGTAA SEQ2> CGNNGTAG SCORE> 5 WEIGHT> 6 ERROR> 0.166667 SEQ1> CGGCGTAA SEQ3> CGGC--AA SCORE> 6 WEIGHT> 8 ERROR> 0.250000 SEQ1> CGGCGTAA SEQ4> CGNN--AG SCORE> 3 WEIGHT> 6 ERROR> 0.500000 SEQ1> CGGCGTAA SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ6> NNNNNNAA SCORE> 2 WEIGHT> 2 ERROR> 0.000000 SEQ1> CGGCGTAA SEQ7> -------- SCORE> 0 WEIGHT> 8 ERROR> 1.000000 SEQ1> CGGCGTAA SEQ8> CG------ SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ2> CGNNGTAG SEQ3> CGGC--AA SCORE> 3 WEIGHT> 6 ERROR> 0.500000 SEQ2> CGNNGTAG SEQ4> CGNN--AG SCORE> 4 WEIGHT> 6 ERROR> 0.333333 SEQ2> CGNNGTAG SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ6> NNNNNNAA SCORE> 1 WEIGHT> 2 ERROR> 0.500000 SEQ2> CGNNGTAG SEQ7> -------- SCORE> 0 WEIGHT> 6 ERROR> 1.000000 SEQ2> CGNNGTAG SEQ8> CG------ SCORE> 2 WEIGHT> 6 ERROR> 0.666667 SEQ3> CGGC--AA SEQ4> CGNN--AG SCORE> 5 WEIGHT> 6 ERROR> 0.166667 SEQ3> CGGC--AA SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ3> CGGC--AA SEQ6> NNNNNNAA SCORE> 2 WEIGHT> 2 ERROR> 0.000000 SEQ3> CGGC--AA SEQ7> -------- SCORE> 2 WEIGHT> 8 ERROR> 0.750000 SEQ3> CGGC--AA SEQ8> CG------ SCORE> 4 WEIGHT> 8 ERROR> 0.500000 SEQ4> CGNN--AG SEQ5> NNNNNNNN SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ4> CGNN--AG SEQ6> NNNNNNAA SCORE> 1 WEIGHT> 2 ERROR> 0.500000 SEQ4> CGNN--AG SEQ7> -------- SCORE> 2 WEIGHT> 6 ERROR> 0.666667 SEQ4> CGNN--AG SEQ8> CG------ SCORE> 4 WEIGHT> 6 ERROR> 0.333333 SEQ5> NNNNNNNN SEQ6> NNNNNNAA SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ7> -------- SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ5> NNNNNNNN SEQ8> CG------ SCORE> 0 WEIGHT> 0 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ7> -------- SCORE> 0 WEIGHT> 2 ERROR> 1.000000 SEQ6> NNNNNNAA SEQ8> CG------ SCORE> 0 WEIGHT> 2 ERROR> 1.000000 SEQ7> -------- SEQ8> CG------ SCORE> 6 WEIGHT> 8 ERROR> 0.250000 <- test_scoreSeqPair() 0.022 -> 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() 0.002 -> 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:305: /usr/bin/python3.12 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 creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12 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/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/Annotation.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/presto/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/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 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__/__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__/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__/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__/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__/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__/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__/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__/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__/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/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/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/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/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/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/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/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/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/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/ParseLog.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__/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__/UnifyHeaders.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/MaskPrimers.cpython-312.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/__pycache__/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__/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/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/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/AssemblePairs.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/CollapseSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.12_presto/build/bin/ParseHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/Annotation.py to Annotation.cpython-312.pyc /usr/lib/python3.12/dist-packages/presto/Annotation.py:293: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/presto/Annotation.py:368: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/presto/Annotation.py:491: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/presto/Annotation.py:493: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/presto/Annotation.py:494: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/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/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/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 /usr/lib/python3.12/dist-packages/presto/IO.py:34: SyntaxWarning: invalid escape sequence '\s' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/presto/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 /usr/lib/python3.12/dist-packages/presto/Applications.py:61: SyntaxWarning: invalid escape sequence '\.' /usr/lib/python3.12/dist-packages/presto/Applications.py:288: SyntaxWarning: invalid escape sequence '\>' byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/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/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/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/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/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/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/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/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/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/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/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/AssemblePairs.py to AssemblePairs.cpython-312.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.12/dist-packages/bin/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/ParseHeaders.py to ParseHeaders.cpython-312.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/python3.12/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-3.12/ConvertHeaders.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/FilterSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/BuildConsensus.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/PairSeq.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/SplitSeq.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/ParseLog.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/UnifyHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/AssemblePairs.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.12/CollapseSeq.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 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/ClusterSets.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/BuildConsensus.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/AlignSets.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/MaskPrimers.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/EstimateError.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/AssemblePairs.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/ParseHeaders.py to 755 I: pybuild base:305: /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/python3.11 creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto/Annotation.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto/Defaults.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto/Sequence.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto/Multiprocessing.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto/__pycache__/Commandline.cpython-311.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto/__pycache__/Sequence.cpython-311.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto/__pycache__/Defaults.cpython-311.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto/__pycache__/IO.cpython-311.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto/__pycache__/Annotation.cpython-311.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto/__pycache__/Version.cpython-311.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto/__pycache__/Multiprocessing.cpython-311.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto/__pycache__/Applications.cpython-311.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto/Version.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto/__init__.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto/IO.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto/Commandline.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/presto/Applications.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/ConvertHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/ClusterSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/FilterSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/BuildConsensus.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/PairSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/AlignSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/SplitSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/MaskPrimers.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/ParseLog.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin creating /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/__pycache__/MaskPrimers.cpython-311.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/__pycache__/AssemblePairs.cpython-311.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/__pycache__/UnifyHeaders.cpython-311.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/__pycache__/BuildConsensus.cpython-311.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/__pycache__/ConvertHeaders.cpython-311.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/__pycache__/EstimateError.cpython-311.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/__pycache__/CollapseSeq.cpython-311.pyc -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/__pycache__ copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/EstimateError.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/UnifyHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/AssemblePairs.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/CollapseSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin copying /build/reproducible-path/presto-0.7.2/.pybuild/cpython3_3.11_presto/build/bin/ParseHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/Annotation.py to Annotation.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/Defaults.py to Defaults.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/Sequence.py to Sequence.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/Multiprocessing.py to Multiprocessing.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/Version.py to Version.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/IO.py to IO.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/Commandline.py to Commandline.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/presto/Applications.py to Applications.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/ConvertHeaders.py to ConvertHeaders.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/ClusterSets.py to ClusterSets.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/FilterSeq.py to FilterSeq.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/BuildConsensus.py to BuildConsensus.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/PairSeq.py to PairSeq.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/AlignSets.py to AlignSets.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/SplitSeq.py to SplitSeq.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/MaskPrimers.py to MaskPrimers.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/ParseLog.py to ParseLog.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/EstimateError.py to EstimateError.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/UnifyHeaders.py to UnifyHeaders.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/AssemblePairs.py to AssemblePairs.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/CollapseSeq.py to CollapseSeq.cpython-311.pyc byte-compiling /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/lib/python3.11/dist-packages/bin/ParseHeaders.py to ParseHeaders.cpython-311.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/python3.11/dist-packages/presto-0.7.2.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.11/ConvertHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.11/ClusterSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.11/FilterSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.11/BuildConsensus.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.11/PairSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.11/AlignSets.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.11/SplitSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.11/MaskPrimers.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.11/ParseLog.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.11/EstimateError.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.11/UnifyHeaders.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.11/AssemblePairs.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.11/CollapseSeq.py -> /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin copying build/scripts-3.11/ParseHeaders.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/ConvertHeaders.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/FilterSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/BuildConsensus.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/PairSeq.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/SplitSeq.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/ParseLog.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/UnifyHeaders.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/AssemblePairs.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/CollapseSeq.py to 755 changing mode of /build/reproducible-path/presto-0.7.2/debian/python3-presto/usr/bin/ParseHeaders.py to 755 debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/presto-0.7.2' dh_install mkdir -p debian/presto/usr mv debian/python3-presto/usr/bin debian/presto/usr make[1]: Leaving directory '/build/reproducible-path/presto-0.7.2' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/presto-0.7.2' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/presto-0.7.2' dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-presto' in '../python3-presto_0.7.2-1_armhf.deb'. dpkg-deb: building package 'presto' in '../presto_0.7.2-1_all.deb'. dpkg-genbuildinfo --build=binary -O../presto_0.7.2-1_armhf.buildinfo dpkg-genchanges --build=binary -O../presto_0.7.2-1_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: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/9350/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/9350/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/9350 and its subdirectories I: Current time: Thu Apr 4 15:40:46 +14 2024 I: pbuilder-time-stamp: 1712194846