I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 4 11:51:11 +14 2024 I: pbuilder-time-stamp: 1725400271 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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 [tnseq-transit_3.2.1-1.dsc] I: copying [./tnseq-transit_3.2.1.orig.tar.gz] I: copying [./tnseq-transit_3.2.1-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.GdYiCDwF/trustedkeys.kbx': General error gpgv: Signature made Fri Dec 25 08:30:31 2020 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./tnseq-transit_3.2.1-1.dsc dpkg-source: info: extracting tnseq-transit in tnseq-transit-3.2.1 dpkg-source: info: unpacking tnseq-transit_3.2.1.orig.tar.gz dpkg-source: info: unpacking tnseq-transit_3.2.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_test_requiring_non_existing_input_data.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2123324/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. 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 Sep 4 11:51 /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/2123324/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2123324/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16 ' DIRSTACK=() DISTRIBUTION=bullseye EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=18e02b8e480448658bdbf632d19db1c5 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2123324 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.r2rmUt7B/pbuilderrc_jQWu --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.r2rmUt7B/b2 --logfile b2/build.log tnseq-transit_3.2.1-1.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.38-2 (2023-07-27) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jan 21 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 21 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 8 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jan 21 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 21 2022 more -rwsr-xr-x 1 root root 55528 Jan 21 2022 mount -rwxr-xr-x 1 root root 18664 Jan 21 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 9 Sep 4 11:51 sh -> /bin/bash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jan 21 2022 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 21 2022 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 21 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/2123324/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3-dev, python3-setuptools, python3-numpy, python3-scipy, python3-pil, python3-matplotlib, python3-statsmodels, python3-pubsub, bwa dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19707 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-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-pil; however: Package python3-pil is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-statsmodels; however: Package python3-statsmodels is not installed. pbuilder-satisfydepends-dummy depends on python3-pubsub; however: Package python3-pubsub is not installed. pbuilder-satisfydepends-dummy depends on bwa; however: Package bwa 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} bwa{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fonts-lyx{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfreetype6{a} libgfortran5{a} libicu67{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{a} libpipeline1{a} libpng16-16{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.9{a} libpython3.9-dev{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} libsigsegv2{a} libsub-override-perl{a} libtiff5{a} libtool{a} libuchardet0{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} po-debconf{a} python-matplotlib-data{a} python3{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-kiwisolver{a} python3-lib2to3{a} python3-matplotlib{a} python3-minimal{a} python3-numpy{a} python3-pandas{a} python3-pandas-lib{a} python3-patsy{a} python3-pil{a} python3-pkg-resources{a} python3-pubsub{a} python3-pyparsing{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-statsmodels{a} python3-statsmodels-lib{a} python3-tz{a} python3.9{a} python3.9-dev{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} ttf-bitstream-vera{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx python3-bottleneck python3-bs4 python3-colorama python3-cvxopt python3-html5lib python3-jinja2 python3-joblib python3-lxml python3-numba python3-numexpr python3-odf python3-olefile python3-openpyxl python3-tables python3-tk python3-xlwt wget 0 packages upgraded, 103 newly installed, 0 to remove and 0 not upgraded. Need to get 73.7 MB of archives. After unpacking 297 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 mailcap all 3.69 [31.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 mime-support all 3.66 [10.9 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 bwa amd64 0.7.17-6+b1 [212 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 python3-distutils all 3.9.2-1 [143 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 fonts-lyx all 2.3.6-1 [205 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3 [153 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libexpat1-dev amd64 2.2.10-2+deb11u5 [141 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 libimagequant0 amd64 2.12.2-1.1 [32.5 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery-ui all 1.12.1+dfsg-8+deb11u1 [232 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3 [2166 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 liblbfgsb0 amd64 3.0+dfsg.3-9 [28.5 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 liblcms2-2 amd64 2.12~rc1-2 [150 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libpython3.9 amd64 3.9.2-1 [1691 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-dev amd64 3.9.2-1 [4028 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libpython3-dev amd64 3.9.2-3 [21.7 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1 [258 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u4 [290 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libwebpdemux2 amd64 0.6.1-2.1 [87.7 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libwebpmux3 amd64 0.6.1-2.1 [97.6 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 ttf-bitstream-vera all 1.10-8.1 [223 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 python-matplotlib-data all 3.3.4-1 [4153 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 python3-six all 1.16.0-2 [17.5 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 python3-cycler all 0.10.0-3 [8084 B] Get: 84 http://deb.debian.org/debian bullseye/main amd64 python3-dateutil all 2.8.1-6 [79.2 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 python3-decorator all 4.4.2-2 [15.8 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 python3.9-dev amd64 3.9.2-1 [515 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 python3-dev amd64 3.9.2-3 [24.8 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 python3-kiwisolver amd64 1.3.1-1+b1 [55.7 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 python3-pyparsing all 2.4.7-1 [109 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 python3-numpy amd64 1:1.19.5-1 [2693 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 python3-pil amd64 8.1.2+dfsg-0.3+deb11u1 [445 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 python3-matplotlib amd64 3.3.4-1 [4163 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 python3-tz all 2021.1-1 [34.8 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 python3-pandas-lib amd64 1.1.5+dfsg-2 [3287 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 python3-pandas all 1.1.5+dfsg-2 [2096 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 python3-patsy all 0.5.1-3 [172 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 python3-pubsub all 4.0.3-4 [46.6 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 python3-scipy amd64 1.6.0-2 [12.3 MB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 python3-setuptools all 52.0.0-4 [366 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 python3-statsmodels-lib amd64 0.12.2-1 [1366 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 python3-statsmodels all 0.12.2-1 [4455 kB] Fetched 73.7 MB in 1s (80.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19707 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. 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Setting up libexpat1:amd64 (2.2.10-2+deb11u5) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20574 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... 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Setting up bsdextrautils (2.36.1-8+deb11u1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up bwa (0.7.17-6+b1) ... Setting up fonts-lyx (2.3.6-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:amd64 (3.9.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libexpat1-dev:amd64 (2.2.10-2+deb11u5) ... Setting up libjpeg62-turbo:amd64 (1:2.0.6-4) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up libpng16-16:amd64 (1.6.37-3) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:amd64 (0.6.1-2.1) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2+deb11u2) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libtiff5:amd64 (4.2.0-1+deb11u4) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up python-matplotlib-data (3.3.4-1) ... Setting up libwebpmux3:amd64 (0.6.1-2.1) ... Setting up libbsd0:amd64 (0.11.3-1) ... Setting up mailcap (3.69) ... Setting up libelf1:amd64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.9.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.6-15) ... Setting up libwebpdemux2:amd64 (0.6.1-2.1) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libjs-jquery-ui (1.12.1+dfsg-8+deb11u1) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.3-9) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up libpython3.9:amd64 (3.9.2-1) ... Setting up python3.9 (3.9.2-1) ... Setting up libpython3.9-dev:amd64 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up python3-tz (2021.1-1) ... Setting up python3-six (1.16.0-2) ... Setting up python3-pil:amd64 (8.1.2+dfsg-0.3+deb11u1) ... Setting up python3-decorator (4.4.2-2) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-cycler (0.10.0-3) ... Setting up python3-kiwisolver (1.3.1-1+b1) ... Setting up python3-pubsub (4.0.3-4) ... Setting up python3.9-dev (3.9.2-1) ... Setting up python3-dateutil (2.8.1-6) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up libpython3-dev:amd64 (3.9.2-3) ... Setting up python3-setuptools (52.0.0-4) ... Setting up python3-dev (3.9.2-3) ... Setting up python3-numpy (1:1.19.5-1) ... Setting up python3-statsmodels-lib:amd64 (0.12.2-1) ... Setting up python3-matplotlib (3.3.4-1) ... Setting up python3-scipy (1.6.0-2) ... Setting up python3-pandas-lib:amd64 (1.1.5+dfsg-2) ... Setting up python3-patsy (0.5.1-3) ... Setting up python3-pandas (1.1.5+dfsg-2) ... Setting up python3-statsmodels (0.12.2-1) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... 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/2123324/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bullseye I: user script /srv/workspace/pbuilder/2123324/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/tnseq-transit-3.2.1/ && 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 > ../tnseq-transit_3.2.1-1_source.changes dpkg-buildpackage: info: source package tnseq-transit dpkg-buildpackage: info: source version 3.2.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/tnseq-transit-3.2.1' dh_auto_clean I: pybuild base:232: python3.9 setup.py clean running clean removing '/build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it rm -rf tests_invalid_data rm -rf tnseq_transit.egg-info make[1]: Leaving directory '/build/tnseq-transit-3.2.1' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild debian/rules override_dh_auto_configure make[1]: Entering directory '/build/tnseq-transit-3.2.1' mkdir -p tests_invalid_data mv tests/H37Rv.fna tests_invalid_data dh_auto_configure I: pybuild base:232: python3.9 setup.py config running config make[1]: Leaving directory '/build/tnseq-transit-3.2.1' dh_auto_build -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/view_trash.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/trash.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/transit_tools.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/transit_gui.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/tnseq_tools.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/stat_tools.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/qcDisplay.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/norm_tools.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/images.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/fileDisplay.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/draw_trash.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/__main__.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit copying src/pytransit/__init__.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit creating /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytpp copying src/pytpp/tpp_tools.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytpp copying src/pytpp/tpp_gui.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytpp copying src/pytpp/__main__.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytpp copying src/pytpp/__init__.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytpp creating /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export copying src/pytransit/export/prot_table.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export copying src/pytransit/export/mean_counts.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export copying src/pytransit/export/igv.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export copying src/pytransit/export/combined_wig.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export copying src/pytransit/export/base.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export copying src/pytransit/export/__init__.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export creating /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/convert copying src/pytransit/convert/gff_to_prot_table.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/convert copying src/pytransit/convert/base.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/convert copying src/pytransit/convert/__init__.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/convert creating /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/zinb.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/utest.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/tnseq_stats.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/tn5gaps.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/resampling.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/rankproduct.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/pathway_enrichment.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/normalize.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/norm.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/hmm.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/heatmap.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/gumbel.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/griffin.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/gi.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/example.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/corrplot.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/binomial.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/base.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/anova.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis copying src/pytransit/analysis/__init__.py -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis running egg_info creating tnseq_transit.egg-info writing tnseq_transit.egg-info/PKG-INFO writing dependency_links to tnseq_transit.egg-info/dependency_links.txt writing entry points to tnseq_transit.egg-info/entry_points.txt writing requirements to tnseq_transit.egg-info/requires.txt writing top-level names to tnseq_transit.egg-info/top_level.txt writing manifest file 'tnseq_transit.egg-info/SOURCES.txt' reading manifest file 'tnseq_transit.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'VERSION' warning: no files found matching '*.html' under directory 'src/pytransit/doc/build/html' warning: no files found matching '*.png' under directory 'src/pytransit/doc/build/html/_images' warning: no files found matching '*' under directory 'src/pytransit/doc/build/html/_modules' warning: no files found matching '*' under directory 'src/pytransit/doc/build/html/_static' writing manifest file 'tnseq_transit.egg-info/SOURCES.txt' creating /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/COG_roles.dat -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/GO_associated_Rvs-3-11-18.txt -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/GO_associated_Rvs.csv -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/GO_term_names.dat -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/GO_terms_for_each_Rv.obo-3-11-18.txt -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/H37Rv.sanger_associated_RVS.csv -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/H37Rv_COG_roles.dat -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/H37Rv_GO_terms.txt -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/H37Rv_sanger_roles.dat -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/README.md -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/cholesterol_H37Rv_merged.wig -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/cholesterol_H37Rv_rep1.wig -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/cholesterol_H37Rv_rep2.wig -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/cholesterol_H37Rv_rep3.wig -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/cholesterol_glycerol_combined.dat -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/gene_ontology.1_2.3-11-18.obo -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/glycerol_H37Rv_merged.wig -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/glycerol_H37Rv_rep1.wig -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/glycerol_H37Rv_rep2.wig -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/samples_metadata_cg.txt -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/samples_metadata_cg_covar.txt -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/samples_metadata_cg_interactions.txt -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/sanger_roles.dat -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data copying src/pytransit/data/smeg_GO_terms.txt -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data creating /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/BCG.fna -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/BCG.prot_table -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/H37Rv.fna -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/H37Rv.prot_table -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/H37RvBD.fna -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/H37RvBD.prot_table -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/H37RvBD_mod3.prot_table -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/H37RvMA2.fna -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/H37RvMA2.prot_table -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/genomes.html -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/mc2_155_tamu.fna -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes copying src/pytransit/genomes/mc2_155_tamu.prot_table -> /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes debian/rules override_dh_auto_test make[1]: Entering directory '/build/tnseq-transit-3.2.1' dh_auto_test -- --system=custom --test-args="PYTHONPATH=tests {interpreter} -m unittest -v tests/*.py" I: pybuild base:232: PYTHONPATH=tests python3.9 -m unittest -v tests/*.py /build/tnseq-transit-3.2.1/tests/../src/pytpp/tpp_tools.py:648: SyntaxWarning: "is" with a literal. Did you mean "=="? if vars.num_replicons is 1: /build/tnseq-transit-3.2.1/tests/../src/pytpp/tpp_tools.py:651: SyntaxWarning: "is" with a literal. Did you mean "=="? elif len(vars.replicon_ids) is 1 and vars.replicon_ids[0].strip() == 'auto': test_Binomial (tests.test_analysis_methods.TestMethods) ... /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/glycerol_H37Rv_rep1.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/glycerol_H37Rv_rep2.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/glycerol_H37Rv_rep1.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/glycerol_H37Rv_rep2.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:1287: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.prot_table' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:1214: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.prot_table' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:518: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.prot_table' mode='r' encoding='UTF-8'> for line in open(self.annotation): ResourceWarning: Enable tracemalloc to get the object allocation traceback #################### tests.test_analysis_methods.TestMethods.test_Binomial #################### [binomial] Starting Binomial Method [binomial] Getting Data [binomial] Setting Parameters [binomial] Setting Initial Values [binomial] Running Binomial Method... 0.2% [binomial] Running Binomial Method... 0.3% [binomial] Running Binomial Method... 0.4% [binomial] Running Binomial Method... 0.5% [binomial] Running Binomial Method... 0.5% [binomial] Running Binomial Method... 0.6% [binomial] 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[binomial] Running Binomial Method... 83.4% [binomial] Running Binomial Method... 83.5% [binomial] Running Binomial Method... 83.5% [binomial] Running Binomial Method... 83.6% [binomial] Running Binomial Method... 83.7% [binomial] Running Binomial Method... 83.8% [binomial] Running Binomial Method... 83.9% [binomial] Running Binomial Method... 84.0% [binomial] Running Binomial Method... 84.1% [binomial] Running Binomial Method... 84.2% [binomial] Running Binomial Method... 84.3% [binomial] Running Binomial Method... 84.4% [binomial] Running Binomial Method... 84.5% [binomial] Running Binomial Method... 84.5% [binomial] Running Binomial Method... 84.6% [binomial] Running Binomial Method... 84.7% [binomial] Running Binomial Method... 84.8% [binomial] Running Binomial Method... 84.9% [binomial] Running Binomial Method... 85.0% [binomial] Running Binomial Method... 85.1% [binomial] Running Binomial Method... 85.2% [binomial] Running Binomial Method... 85.3% [binomial] Running Binomial 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Running Binomial Method... 99.8% [binomial] Running Binomial Method... 99.9% [binomial] Running Binomial Method... 100.0% ok test_GI (tests.test_analysis_methods.TestMethods) ... /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep1.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep2.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep3.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep1.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep2.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep3.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback [binomial] [binomial] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [binomial] Finished Binomial Method Removing output file... #################### tests.test_analysis_methods.TestMethods.test_GI #################### [gi] Starting Genetic Interactions Method [gi] Getting Data [gi] Normalizing using: TTR [gi] Running GI Method... 2% [gi] Running Export Method... 0.0% [gi] Running GI Method... 4% [gi] Running Export Method... 2.0% [gi] Running GI Method... 6% [gi] Running Export Method... 4.0% [gi] Running GI Method... 8% [gi] Running Export Method... 6.0% [gi] Running GI Method... 10% [gi] Running Export Method... 8.0% [gi] Running GI Method... 12% [gi] Running Export Method... 10.0% [gi] Running GI Method... 14% [gi] Running Export 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<_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/testoutput.txt' mode='w' encoding='UTF-8'> method() ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_Griffin (tests.test_analysis_methods.TestMethods) ... 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sigma_s) * (1-w1)) [griffin] [griffin] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [griffin] Finished Griffin Method Removing output file... #################### tests.test_analysis_methods.TestMethods.test_Gumbel #################### [gumbel] Reading Annotation [gumbel] Getting Data [gumbel] Doing Regression [gumbel] Setting Initial Class [gumbel] Running Gumbel Method... 0.2% [gumbel] Running Gumbel Method... 0.3% [gumbel] Running Gumbel Method... 0.4% [gumbel] Running Gumbel Method... 0.5% [gumbel] Running Gumbel Method... 0.5% [gumbel] Running Gumbel Method... 0.6% [gumbel] Running Gumbel Method... 0.7% [gumbel] Running Gumbel Method... 0.8% [gumbel] Running Gumbel Method... 0.9% [gumbel] Running Gumbel Method... 1.0% [gumbel] Running Gumbel Method... 1.1% [gumbel] Running Gumbel Method... 1.2% [gumbel] Running Gumbel Method... 1.3% [gumbel] Running Gumbel Method... 1.4% [gumbel] Running Gumbel Method... 1.5% [gumbel] Running Gumbel Method... 1.5% [gumbel] Running 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Method... 97.3% [gumbel] Running Gumbel Method... 97.4% [gumbel] Running Gumbel Method... 97.5% [gumbel] Running Gumbel Method... 97.5% [gumbel] Running Gumbel Method... 97.6% [gumbel] Running Gumbel Method... 97.7% [gumbel] Running Gumbel Method... 97.8% [gumbel] Running Gumbel Method... 97.9% [gumbel] Running Gumbel Method... 98.0% [gumbel] Running Gumbel Method... 98.1% [gumbel] Running Gumbel Method... 98.2% [gumbel] Running Gumbel Method... 98.3% [gumbel] Running Gumbel Method... 98.4% [gumbel] Running Gumbel Method... 98.5% [gumbel] Running Gumbel Method... 98.5% [gumbel] Running Gumbel Method... 98.6% [gumbel] Running Gumbel Method... 98.7% [gumbel] Running Gumbel Method... 98.8% [gumbel] Running Gumbel Method... 98.9% [gumbel] Running Gumbel Method... 99.0% [gumbel] Running Gumbel Method... 99.1% [gumbel] Running Gumbel Method... 99.2% [gumbel] Running Gumbel Method... 99.3% [gumbel] Running Gumbel Method... 99.4% [gumbel] Running Gumbel Method... 99.5% [gumbel] Running Gumbel Method... 99.5% [gumbel] Running Gumbel Method... 99.6% [gumbel] Running Gumbel Method... 99.7% [gumbel] Running Gumbel Method... 99.8% [gumbel] Running Gumbel Method... 99.9% [gumbel] Running Gumbel Method... 100.0% ok test_HMM (tests.test_analysis_methods.TestMethods) ... /build/tnseq-transit-3.2.1/tests/../src/pytransit/analysis/hmm.py:194: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.wig' mode='r' encoding='UTF-8'> T = len([1 for line in open(ctrldata[0]).readlines() if not line.startswith("#")]) ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback [gumbel] [gumbel] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [gumbel] Finished Gumbel Method Removing output file... #################### tests.test_analysis_methods.TestMethods.test_HMM #################### [hmm] Starting HMM Method [hmm] Getting Data [hmm] Normalizing using: TTR [hmm] Running HMM Method... 2.5% [hmm] Running HMM Method... 5.0% [hmm] Running HMM Method... 7.5% [hmm] Running HMM Method... 10.0% [hmm] Running HMM Method... 12.5% [hmm] Running HMM Method... 15.0% [hmm] Running HMM Method... 17.5% [hmm] Running HMM Method... 20.0% [hmm] Running HMM Method... 22.5% [hmm] Running HMM Method... 25.0% [hmm] Running HMM Method... 27.5% [hmm] Running HMM Method... 30.0% [hmm] Running HMM Method... 32.5% [hmm] Running HMM Method... 35.0% [hmm] Running HMM Method... 37.5% [hmm] Running HMM Method... 40.0% [hmm] Running HMM Method... 42.5% [hmm] Running HMM Method... 45.0% [hmm] Running HMM Method... 47.5% [hmm] Running HMM Method... 50.0% [hmm] Running HMM Method... 50.0% [hmm] Running HMM Method... 52.5% [hmm] Running HMM Method... 55.0% [hmm] Running HMM Method... 57.5% [hmm] Running HMM Method... 60.0% [hmm] Running HMM Method... 62.5% [hmm] Running HMM Method... 65.0% [hmm] Running HMM Method... 67.5% [hmm] Running HMM Method... 70.0% [hmm] Running HMM Method... 72.5% [hmm] Running HMM Method... 75.0% [hmm] Running HMM Method... 77.5% [hmm] Running HMM Method... 80.0% [hmm] Running HMM Method... 82.5% [hmm] Running HMM Method... 85.0% [hmm] Running HMM Method... 87.5% [hmm] Running HMM Method... 90.0% [hmm] Running HMM Method... 92.5% [hmm] Running HMM Method... 95.0% [hmm] Running HMM Method... 97.5% ok test_anova (tests.test_analysis_methods.TestMethods) ... /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:121: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.prot_table' mode='r' encoding='UTF-8'> for line in open(fname): ResourceWarning: Enable tracemalloc to get the object allocation traceback [hmm] [hmm] Finished HMM - Sites Method [hmm] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [hmm] Creating HMM Genes Level Output [hmm] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput_genes.txt [hmm] Finished HMM Method Removing output file... #################### tests.test_analysis_methods.TestMethods.test_anova #################### [anova] Starting Anova analysis [anova] Getting Data [anova] Normalizing using: TTR [anova] Running Anova [anova] Running Anova Method... 2.0% [anova] Running Anova Method... 3.9% [anova] Running Anova Method... 5.9% [anova] Running Anova Method... 7.8% [anova] Running Anova Method... 9.8% [anova] Running Anova Method... 11.8% [anova] Running Anova Method... 13.7% [anova] Running Anova Method... 15.7% [anova] Running Anova Method... 17.6% [anova] Running Anova Method... 19.6% [anova] Running Anova Method... 21.6% [anova] Running Anova Method... 23.5% [anova] Running Anova Method... 25.5% [anova] Running Anova Method... 27.5% [anova] Running Anova Method... 29.4% [anova] Running Anova Method... 31.4% [anova] Running Anova Method... 33.3% [anova] Running Anova Method... 35.3% [anova] Running Anova Method... 37.3% [anova] Running Anova Method... 39.2% [anova] Running Anova Method... 41.2% [anova] Running Anova Method... 43.1% [anova] Running Anova Method... 45.1% [anova] Running Anova Method... 47.1% [anova] Running Anova Method... 49.0% [anova] Running Anova Method... 51.0% [anova] Running Anova Method... 52.9% [anova] Running Anova Method... 54.9% [anova] Running Anova Method... 56.9% [anova] Running Anova Method... 58.8% [anova] Running Anova Method... 60.8% [anova] Running Anova Method... 62.7% [anova] Running Anova Method... 64.7% [anova] Running Anova Method... 66.7% [anova] Running Anova Method... 68.6% [anova] Running Anova Method... 70.6% [anova] Running Anova Method... 72.5% [anova] Running Anova Method... 74.5% [anova] Running Anova Method... 76.5% [anova] Running Anova Method... 78.4% [anova] Running Anova Method... 80.4% [anova] Running Anova Method... 82.4% [anova] Running Anova Method... 84.3% [anova] Running Anova Method... 86.3% [anova] Running Anova Method... 88.2% [anova] Running Anova Method... 90.2% [anova] Running Anova Method... 92.2% [anova] Running Anova Method... 94.1% [anova] Running Anova Method... 96.1% [anova] Running Anova Method... 98.0% [anova] Running Anova Method... 100.0% /build/tnseq-transit-3.2.1/tests/transit_test.py:89: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/testoutput.txt' mode='r' encoding='UTF-8'> for line in open(fname): ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_resampling (tests.test_analysis_methods.TestMethods) ... /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/glycerol_H37Rv_rep1.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/glycerol_H37Rv_rep2.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/glycerol_H37Rv_rep1.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/glycerol_H37Rv_rep2.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep1.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep2.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:910: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep3.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep1.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep2.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:927: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/data/cholesterol_H37Rv_rep3.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:1287: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.prot_table' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:1214: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.prot_table' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:518: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test.prot_table' mode='r' encoding='UTF-8'> for line in open(self.annotation): ResourceWarning: Enable tracemalloc to get the object allocation traceback [anova] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [anova] Finished Anova analysis [anova] Time: 0.7s Removing output file... #################### tests.test_analysis_methods.TestMethods.test_resampling #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: TTR [resampling] Performing LOESS Correction [resampling] Preprocessing Exp data... [resampling] Normalizing using: TTR [resampling] Performing LOESS Correction [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% /build/tnseq-transit-3.2.1/tests/transit_test.py:89: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/testoutput.txt' mode='r' encoding='UTF-8'> for line in open(fname): ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_resampling_adaptive (tests.test_analysis_methods.TestMethods) ... /build/tnseq-transit-3.2.1/tests/../src/pytransit/stat_tools.py:717: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray DATA[K] = numpy.array([L1[K], L2[K]]) /build/tnseq-transit-3.2.1/tests/../src/pytransit/stat_tools.py:515: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray E[L] = numpy.array([perm[:n1], perm[n1:]]) [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing output file... #################### tests.test_analysis_methods.TestMethods.test_resampling_adaptive #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: TTR [resampling] Preprocessing Exp data... [resampling] Normalizing using: TTR [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_resampling_combined_wig (tests.test_analysis_methods.TestMethods) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing output file... #################### tests.test_analysis_methods.TestMethods.test_resampling_combined_wig #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: TTR [resampling] Preprocessing Exp data... [resampling] Normalizing using: TTR [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_resampling_histogram (tests.test_analysis_methods.TestMethods) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method 37 35 Removing output file... #################### tests.test_analysis_methods.TestMethods.test_resampling_histogram #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: TTR [resampling] Preprocessing Exp data... [resampling] Normalizing using: TTR [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_resampling_multistrain (tests.test_analysis_methods.TestMethods) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing histogram files Removing output file... #################### tests.test_analysis_methods.TestMethods.test_resampling_multistrain #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Multiple annotation files found [resampling] Mapping ctrl data to /build/tnseq-transit-3.2.1/tests/data/test.prot_table, exp data to /build/tnseq-transit-3.2.1/tests/data/test.prot_table [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: TTR [resampling] Preprocessing Exp data... [resampling] Normalizing using: TTR [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_utest (tests.test_analysis_methods.TestMethods) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing histogram files Removing output file... #################### tests.test_analysis_methods.TestMethods.test_utest #################### [utest] Starting Mann-Whitney U-test Method [utest] Getting Data [utest] Normalizing using: TTR [utest] Running Mann-Whitney U-test Method... 2.0% [utest] Running Mann-Whitney U-test Method... 3.9% [utest] Running Mann-Whitney U-test Method... 5.9% [utest] Running Mann-Whitney U-test Method... 7.8% [utest] Running Mann-Whitney U-test Method... 9.8% [utest] Running Mann-Whitney U-test Method... 11.8% [utest] Running Mann-Whitney U-test Method... 13.7% [utest] Running Mann-Whitney U-test Method... 15.7% [utest] Running Mann-Whitney U-test Method... 17.6% [utest] Running Mann-Whitney U-test Method... 19.6% [utest] Running Mann-Whitney U-test Method... 21.6% [utest] Running Mann-Whitney U-test Method... 23.5% [utest] Running Mann-Whitney U-test Method... 25.5% [utest] Running Mann-Whitney U-test Method... 27.5% [utest] Running Mann-Whitney U-test Method... 29.4% [utest] Running Mann-Whitney U-test Method... 31.4% [utest] Running Mann-Whitney U-test Method... 33.3% [utest] Running Mann-Whitney U-test Method... 35.3% [utest] Running Mann-Whitney U-test Method... 37.3% [utest] Running Mann-Whitney U-test Method... 39.2% [utest] Running Mann-Whitney U-test Method... 41.2% [utest] Running Mann-Whitney U-test Method... 43.1% [utest] Running Mann-Whitney U-test Method... 45.1% [utest] Running Mann-Whitney U-test Method... 47.1% [utest] Running Mann-Whitney U-test Method... 49.0% [utest] Running Mann-Whitney U-test Method... 51.0% [utest] Running Mann-Whitney U-test Method... 52.9% [utest] Running Mann-Whitney U-test Method... 54.9% [utest] Running Mann-Whitney U-test Method... 56.9% [utest] Running Mann-Whitney U-test Method... 58.8% [utest] Running Mann-Whitney U-test Method... 60.8% [utest] Running Mann-Whitney U-test Method... 62.7% [utest] Running Mann-Whitney U-test Method... 64.7% [utest] Running Mann-Whitney U-test Method... 66.7% [utest] Running Mann-Whitney U-test Method... 68.6% [utest] Running Mann-Whitney U-test Method... 70.6% [utest] Running Mann-Whitney U-test Method... 72.5% [utest] Running Mann-Whitney U-test Method... 74.5% [utest] Running Mann-Whitney U-test Method... 76.5% [utest] Running Mann-Whitney U-test Method... 78.4% [utest] Running Mann-Whitney U-test Method... 80.4% [utest] Running Mann-Whitney U-test Method... 82.4% [utest] Running Mann-Whitney U-test Method... 84.3% [utest] Running Mann-Whitney U-test Method... 86.3% [utest] Running Mann-Whitney U-test Method... 88.2% [utest] Running Mann-Whitney U-test Method... 90.2% [utest] Running Mann-Whitney U-test Method... 92.2% [utest] Running Mann-Whitney U-test Method... 94.1% [utest] Running Mann-Whitney U-test Method... 96.1% [utest] Running Mann-Whitney U-test Method... 98.0% [utest] Running Mann-Whitney U-test Method... 100.0% ok test_zinb (tests.test_analysis_methods.TestMethods) ... skipped 'requires R, rpy2' test_zinb_covariates (tests.test_analysis_methods.TestMethods) ... skipped 'requires R, rpy2' test_zinb_interactions (tests.test_analysis_methods.TestMethods) ... skipped 'requires R, rpy2' test_TTR (tests.test_norm_methods.TestNormMethods) ... ok test_nonorm (tests.test_norm_methods.TestNormMethods) ... ok test_resampling_NZMean (tests.test_norm_methods.TestNormMethods) ... [utest] [utest] Performing Benjamini-Hochberg Correction [utest] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [utest] Finished Mann-Whitney U-test Method Removing output file... #################### tests.test_norm_methods.TestNormMethods.test_TTR #################### #################### tests.test_norm_methods.TestNormMethods.test_nonorm #################### #################### tests.test_norm_methods.TestNormMethods.test_resampling_NZMean #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: nzmean [resampling] Preprocessing Exp data... [resampling] Normalizing using: nzmean [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_resampling_Quantile (tests.test_norm_methods.TestNormMethods) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing output file... #################### tests.test_norm_methods.TestNormMethods.test_resampling_Quantile #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: quantile [resampling] Preprocessing Exp data... [resampling] Normalizing using: quantile [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% /build/tnseq-transit-3.2.1/tests/transit_test.py:75: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/testoutput.txt' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_resampling_TTR (tests.test_norm_methods.TestNormMethods) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing output file... #################### tests.test_norm_methods.TestNormMethods.test_resampling_TTR #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: TTR [resampling] Preprocessing Exp data... [resampling] Normalizing using: TTR [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_resampling_TotReads (tests.test_norm_methods.TestNormMethods) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing output file... #################### tests.test_norm_methods.TestNormMethods.test_resampling_TotReads #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: totreads [resampling] Preprocessing Exp data... [resampling] Normalizing using: totreads [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_resampling_ZINFNB (tests.test_norm_methods.TestNormMethods) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing output file... #################### tests.test_norm_methods.TestNormMethods.test_resampling_ZINFNB #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Normalizing using: zinfnb [resampling] Preprocessing Exp data... [resampling] Normalizing using: zinfnb [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_resampling_nonorm (tests.test_norm_methods.TestNormMethods) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing output file... #################### tests.test_norm_methods.TestNormMethods.test_resampling_nonorm #################### [resampling] Starting resampling Method [resampling] Getting Data [resampling] Preprocessing Ctrl data... [resampling] Preprocessing Exp data... [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_cleanargs_flag_arguments_w_quotes (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_cleanargs_flag_arguments_with_double_dash (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_cleanargs_flag_without_arguments (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_cleanargs_negative_arguments (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_cleanargs_positional_arguments (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_cleanargs_positional_arguments_w_quotes (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_file_types (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_genes_creation_fromdata (tests.test_pytransit_tools.TestTnSeqTools) ... /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:1287: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/genomes/H37Rv.prot_table' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:1214: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/genomes/H37Rv.prot_table' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytransit/tnseq_tools.py:518: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/../src/pytransit/genomes/H37Rv.prot_table' mode='r' encoding='UTF-8'> for line in open(self.annotation): ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_genes_creation_fromwig (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_normalization (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_read_data (tests.test_pytransit_tools.TestTnSeqTools) ... ok test_tpp_flag_primer (tests.test_tpp.TestTPP) ... skipped 'requires local data file' test_tpp_multicontig_auto_replicon_ids (tests.test_tpp.TestTPP) ... [tn_preprocess] running pre-processing on /build/tnseq-transit-3.2.1/tests/data/test-multicontig-1.fastq and [tn_preprocess] protocol: Sassetti [tn_preprocess] transposon type: Himar1 [tn_preprocess] One reference genome specified: /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna, containing 3 records. [tn_preprocess] Autogenerating replicon_ids... [tn_preprocess] extracting reads... [tn_preprocess] fastq2reads: /build/tnseq-transit-3.2.1/tests/data/test-multicontig-1.fastq -> /build/tnseq-transit-3.2.1/tests/test_tpp_temp.reads1 /build/tnseq-transit-3.2.1/tests/../src/pytpp/tpp_tools.py:85: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test-multicontig-1.fastq' mode='r' encoding='UTF-8'> for line in open(infile): ResourceWarning: Enable tracemalloc to get the object allocation traceback [tn_preprocess] assuming single-ended reads [tn_preprocess] creating /build/tnseq-transit-3.2.1/tests/test_tpp_temp.trimmed1 [tn_preprocess] prefix sequence: [tn_preprocess] Looking for start of Tn prefix within P,Q = [0,20] /build/tnseq-transit-3.2.1/tests/../src/pytpp/tpp_tools.py:276: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/test_tpp_temp.reads1' mode='r' encoding='UTF-8'> for line in open(infile): ResourceWarning: Enable tracemalloc to get the object allocation traceback [tn_preprocess] mapping reads using BWA...(this takes a couple of minutes) [tn_preprocess] /usr/bin/bwa index /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna b'[bwa_index] Pack FASTA... 0.05 sec' b'[bwa_index] Construct BWT for the packed sequence...' b'[bwa_index] 2.15 seconds elapse.' b'[bwa_index] Update BWT... 0.04 sec' b'[bwa_index] Pack forward-only FASTA... 0.04 sec' b'[bwa_index] Construct SA from BWT and Occ... 0.88 sec' b'[main] Version: 0.7.17-r1188' b'[main] CMD: /usr/bin/bwa index /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna' b'[main] Real time: 3.154 sec; CPU: 3.160 sec' b'' [tn_preprocess] /usr/bin/bwa mem /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna /build/tnseq-transit-3.2.1/tests/test_tpp_temp.trimmed1 > /build/tnseq-transit-3.2.1/tests/test_tpp_temp.sam b'[M::bwa_idx_load_from_disk] read 0 ALT contigs' b'[M::process] read 2500 sequences (304052 bp)...' b'[M::mem_process_seqs] Processed 2500 reads in 0.216 CPU sec, 0.216 real sec' b'[main] Version: 0.7.17-r1188' b'[main] CMD: /usr/bin/bwa mem /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna /build/tnseq-transit-3.2.1/tests/test_tpp_temp.trimmed1' b'[main] Real time: 0.232 sec; CPU: 0.239 sec' b'' [tn_preprocess] tabulating template counts and statistics for reference genome /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna /build/tnseq-transit-3.2.1/tests/../src/pytpp/tpp_tools.py:378: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna' mode='r' encoding='UTF-8'> for line in open(filename): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytpp/tpp_tools.py:560: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/test_tpp_temp.sam' mode='r' encoding='UTF-8'> for line in open(sam): ResourceWarning: Enable tracemalloc to get the object allocation traceback [tn_preprocess] writing /build/tnseq-transit-3.2.1/tests/test_tpp_temp_1.wig [tn_preprocess] writing /build/tnseq-transit-3.2.1/tests/test_tpp_temp_2.wig [tn_preprocess] writing /build/tnseq-transit-3.2.1/tests/test_tpp_temp_3.wig /build/tnseq-transit-3.2.1/tests/../src/pytpp/tpp_tools.py:1108: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/test_tpp_temp.reads1' mode='r' encoding='UTF-8'> for line in open(vars.reads1): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytpp/tpp_tools.py:1117: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/test_tpp_temp.reads1' mode='r' encoding='UTF-8'> read_length = get_read_length(vars.base + ".reads1") ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/tnseq-transit-3.2.1/tests/../src/pytpp/tpp_tools.py:1118: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/tnseq-transit-3.2.1/tests/test_tpp_temp.trimmed1' mode='r' encoding='UTF-8'> mean_r1_genomic = get_genomic_portion(vars.base + ".trimmed1") ResourceWarning: Enable tracemalloc to get the object allocation traceback [tn_preprocess] writing /build/tnseq-transit-3.2.1/tests/test_tpp_temp.tn_stats [tn_preprocess] Done. ok test_tpp_multicontig_empty_prefix (tests.test_tpp.TestTPP) ... [tn_preprocess] running pre-processing on /build/tnseq-transit-3.2.1/tests/data/test-multicontig-1.fastq and [tn_preprocess] protocol: Sassetti [tn_preprocess] transposon type: Himar1 [tn_preprocess] One reference genome specified: /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna, containing 3 records. [tn_preprocess] extracting reads... [tn_preprocess] fastq2reads: /build/tnseq-transit-3.2.1/tests/data/test-multicontig-1.fastq -> /build/tnseq-transit-3.2.1/tests/test_tpp_temp.reads1 [tn_preprocess] assuming single-ended reads [tn_preprocess] creating /build/tnseq-transit-3.2.1/tests/test_tpp_temp.trimmed1 [tn_preprocess] prefix sequence: [tn_preprocess] Looking for start of Tn prefix within P,Q = [0,20] [tn_preprocess] mapping reads using BWA...(this takes a couple of minutes) [tn_preprocess] /usr/bin/bwa mem /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna /build/tnseq-transit-3.2.1/tests/test_tpp_temp.trimmed1 > /build/tnseq-transit-3.2.1/tests/test_tpp_temp.sam b'[M::bwa_idx_load_from_disk] read 0 ALT contigs' b'[M::process] read 2500 sequences (304052 bp)...' b'[M::mem_process_seqs] Processed 2500 reads in 0.213 CPU sec, 0.214 real sec' b'[main] Version: 0.7.17-r1188' b'[main] CMD: /usr/bin/bwa mem /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna /build/tnseq-transit-3.2.1/tests/test_tpp_temp.trimmed1' b'[main] Real time: 0.229 sec; CPU: 0.236 sec' b'' [tn_preprocess] tabulating template counts and statistics for reference genome /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna [tn_preprocess] writing /build/tnseq-transit-3.2.1/tests/test_tpp_temp_a.wig [tn_preprocess] writing /build/tnseq-transit-3.2.1/tests/test_tpp_temp_b.wig [tn_preprocess] writing /build/tnseq-transit-3.2.1/tests/test_tpp_temp_c.wig [tn_preprocess] writing /build/tnseq-transit-3.2.1/tests/test_tpp_temp.tn_stats [tn_preprocess] Done. ok test_tpp_noflag_primer (tests.test_tpp.TestTPP) ... skipped 'requires local data file' test_tpp_protocol_mme1 (tests.test_tpp.TestTPP) ... skipped 'requires local data file' ---------------------------------------------------------------------- Ran 39 tests in 258.504s OK (skipped=6) [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Adding File: /build/tnseq-transit-3.2.1/tests/testoutput.txt [resampling] Finished resampling Method Removing output file... #################### tests.test_pytransit_tools.TestTnSeqTools.test_cleanargs_flag_arguments_w_quotes #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_cleanargs_flag_arguments_with_double_dash #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_cleanargs_flag_without_arguments #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_cleanargs_negative_arguments #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_cleanargs_positional_arguments #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_cleanargs_positional_arguments_w_quotes #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_file_types #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_genes_creation_fromdata #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_genes_creation_fromwig #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_normalization #################### #################### tests.test_pytransit_tools.TestTnSeqTools.test_read_data #################### #################### tests.test_tpp.TestTPP.test_tpp_multicontig_auto_replicon_ids #################### # title: Tn-Seq Pre-Processor # date: 09/04/2024 11:56:23 # command: python python3.9 -m unittest -v tests/test_analysis_methods.py tests/test_norm_methods.py tests/test_pytransit_tools.py tests/test_tpp.py tests/transit_test.py # transposon type: Himar1 # protocol type: Sassetti # bwa flags: # read1: /build/tnseq-transit-3.2.1/tests/data/test-multicontig-1.fastq # read2: # ref_genome: /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna # replicon_ids: 1,2,3 # total_reads (or read pairs): 2500 # trimmed_reads (reads with valid Tn prefix, and insert size>20bp): 2512 # reads1_mapped: 2116 # reads2_mapped: 0 # mapped_reads (both R1 and R2 map into genome, and R2 has a proper barcode): 2116 # read_count (TA sites only, for Himar1): # 1: 63 # 2: 0 # 3: 0 # template_count: # 1: 63 # 2: 0 # 3: 0 # template_ratio (reads per template): # 1: 1.00 # 2: 0.00 # 3: 0.00 # TA_sites: # 1: 89994 # 2: 646 # 3: 664 # TAs_hit: # 1: 63 # 2: 0 # 3: 0 # density: # 1: 0.001 # 2: 0.000 # 3: 0.000 # max_count (among templates): # 1: 1 # 2: 0 # 3: 0 # max_site (coordinate): # 1: 4977050 # 2: 57441 # 3: 38111 # NZ_mean (among templates): # 1: 1.0 # 2: 0.0 # 3: 0.0 # FR_corr (Fwd templates vs. Rev templates): # 1: -0.000 # 2: nan # 3: nan # BC_corr (reads vs. templates, summed over both strands): # 1: nan # 2: nan # 3: nan # primer_matches: 36 reads (1.4%) contain CTAGAGGGCCCAATTCGCCCTATAGTGAGT (Himar1) # vector_matches: 36 reads (1.4%) contain CTAGACCGTCCAGTCTGGCAGGCCGGAAAC (phiMycoMarT7) # adapter_matches: 57 reads (2.3%) contain GATCGGAAGAGCACACGTCTGAACTCCAGTCAC (Illumina/TruSeq index) # misprimed_reads: 17 reads (0.7%) contain Himar1 prefix but don't end in TGTTA # read_length: 125 bp # mean_R1_genomic_length: 121.6 bp Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file #################### tests.test_tpp.TestTPP.test_tpp_multicontig_empty_prefix #################### # title: Tn-Seq Pre-Processor # date: 09/04/2024 11:56:25 # command: python python3.9 -m unittest -v tests/test_analysis_methods.py tests/test_norm_methods.py tests/test_pytransit_tools.py tests/test_tpp.py tests/transit_test.py # transposon type: Himar1 # protocol type: Sassetti # bwa flags: # read1: /build/tnseq-transit-3.2.1/tests/data/test-multicontig-1.fastq # read2: # ref_genome: /build/tnseq-transit-3.2.1/tests/data/test-multicontig.fna # replicon_ids: a,b,c # total_reads (or read pairs): 2500 # trimmed_reads (reads with valid Tn prefix, and insert size>20bp): 2512 # reads1_mapped: 2116 # reads2_mapped: 0 # mapped_reads (both R1 and R2 map into genome, and R2 has a proper barcode): 2116 # read_count (TA sites only, for Himar1): # a: 63 # b: 0 # c: 0 # template_count: # a: 63 # b: 0 # c: 0 # template_ratio (reads per template): # a: 1.00 # b: 0.00 # c: 0.00 # TA_sites: # a: 89994 # b: 646 # c: 664 # TAs_hit: # a: 63 # b: 0 # c: 0 # density: # a: 0.001 # b: 0.000 # c: 0.000 # max_count (among templates): # a: 1 # b: 0 # c: 0 # max_site (coordinate): # a: 4977050 # b: 57441 # c: 38111 # NZ_mean (among templates): # a: 1.0 # b: 0.0 # c: 0.0 # FR_corr (Fwd templates vs. Rev templates): # a: -0.000 # b: nan # c: nan # BC_corr (reads vs. templates, summed over both strands): # a: nan # b: nan # c: nan # primer_matches: 36 reads (1.4%) contain CTAGAGGGCCCAATTCGCCCTATAGTGAGT (Himar1) # vector_matches: 36 reads (1.4%) contain CTAGACCGTCCAGTCTGGCAGGCCGGAAAC (phiMycoMarT7) # adapter_matches: 57 reads (2.3%) contain GATCGGAAGAGCACACGTCTGAACTCCAGTCAC (Illumina/TruSeq index) # misprimed_reads: 17 reads (0.7%) contain Himar1 prefix but don't end in TGTTA # read_length: 125 bp # mean_R1_genomic_length: 121.6 bp Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file Removing tpp test file make[1]: Leaving directory '/build/tnseq-transit-3.2.1' 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:232: /usr/bin/python3 setup.py install --root /build/tnseq-transit-3.2.1/debian/tnseq-transit running install running build running build_py running egg_info writing tnseq_transit.egg-info/PKG-INFO writing dependency_links to tnseq_transit.egg-info/dependency_links.txt writing entry points to tnseq_transit.egg-info/entry_points.txt writing requirements to tnseq_transit.egg-info/requires.txt writing top-level names to tnseq_transit.egg-info/top_level.txt reading manifest file 'tnseq_transit.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'VERSION' warning: no files found matching '*.html' under directory 'src/pytransit/doc/build/html' warning: no files found matching '*.png' under directory 'src/pytransit/doc/build/html/_images' warning: no files found matching '*' under directory 'src/pytransit/doc/build/html/_modules' warning: no files found matching '*' under directory 'src/pytransit/doc/build/html/_static' writing manifest file 'tnseq_transit.egg-info/SOURCES.txt' running install_lib creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9 creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytpp copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytpp/__init__.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytpp copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytpp/__main__.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytpp copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytpp/tpp_gui.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytpp copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytpp/tpp_tools.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytpp creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/mc2_155_tamu.prot_table -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/mc2_155_tamu.fna -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/genomes.html -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/H37RvMA2.prot_table -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/H37RvMA2.fna -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/H37RvBD_mod3.prot_table -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/H37RvBD.prot_table -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/H37RvBD.fna -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/H37Rv.prot_table -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/H37Rv.fna -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/BCG.prot_table -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/genomes/BCG.fna -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/genomes creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/smeg_GO_terms.txt -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/sanger_roles.dat -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/samples_metadata_cg_interactions.txt -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/samples_metadata_cg_covar.txt -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/samples_metadata_cg.txt -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/glycerol_H37Rv_rep2.wig -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/glycerol_H37Rv_rep1.wig -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/glycerol_H37Rv_merged.wig -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/gene_ontology.1_2.3-11-18.obo -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/cholesterol_glycerol_combined.dat -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/cholesterol_H37Rv_rep3.wig -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/cholesterol_H37Rv_rep2.wig -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/cholesterol_H37Rv_rep1.wig -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/cholesterol_H37Rv_merged.wig -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/README.md -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/H37Rv_sanger_roles.dat -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/H37Rv_GO_terms.txt -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/H37Rv_COG_roles.dat -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/H37Rv.sanger_associated_RVS.csv -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/GO_terms_for_each_Rv.obo-3-11-18.txt -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/GO_term_names.dat -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/GO_associated_Rvs.csv -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/GO_associated_Rvs-3-11-18.txt -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/data/COG_roles.dat -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/data creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/__init__.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/anova.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/base.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/binomial.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/corrplot.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/example.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/gi.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/griffin.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/gumbel.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/heatmap.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/hmm.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/norm.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/normalize.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/pathway_enrichment.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/rankproduct.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/resampling.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/tn5gaps.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/tnseq_stats.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/utest.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/analysis/zinb.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/convert copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/convert/__init__.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/convert copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/convert/base.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/convert copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/convert/gff_to_prot_table.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/convert creating /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export/__init__.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export/base.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export/combined_wig.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export/igv.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export/mean_counts.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/export/prot_table.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/__init__.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/__main__.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/draw_trash.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/fileDisplay.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/images.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/norm_tools.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/qcDisplay.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/stat_tools.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/tnseq_tools.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/transit_gui.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/transit_tools.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/trash.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit copying /build/tnseq-transit-3.2.1/.pybuild/cpython3_3.9/build/pytransit/view_trash.py -> /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytpp/__init__.py to __init__.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytpp/__main__.py to __main__.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytpp/tpp_gui.py to tpp_gui.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytpp/tpp_tools.py to tpp_tools.cpython-39.pyc /usr/lib/python3.9/dist-packages/pytpp/tpp_tools.py:648: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.9/dist-packages/pytpp/tpp_tools.py:651: SyntaxWarning: "is" with a literal. Did you mean "=="? byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/__init__.py to __init__.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/anova.py to anova.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/base.py to base.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/binomial.py to binomial.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/corrplot.py to corrplot.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/example.py to example.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/gi.py to gi.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/griffin.py to griffin.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/gumbel.py to gumbel.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/heatmap.py to heatmap.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/hmm.py to hmm.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/norm.py to norm.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/normalize.py to normalize.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/pathway_enrichment.py to pathway_enrichment.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/rankproduct.py to rankproduct.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/resampling.py to resampling.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/tn5gaps.py to tn5gaps.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/tnseq_stats.py to tnseq_stats.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/utest.py to utest.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/analysis/zinb.py to zinb.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/convert/__init__.py to __init__.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/convert/base.py to base.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/convert/gff_to_prot_table.py to gff_to_prot_table.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export/__init__.py to __init__.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export/base.py to base.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export/combined_wig.py to combined_wig.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export/igv.py to igv.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export/mean_counts.py to mean_counts.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/export/prot_table.py to prot_table.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/__init__.py to __init__.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/__main__.py to __main__.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/draw_trash.py to draw_trash.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/fileDisplay.py to fileDisplay.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/images.py to images.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/norm_tools.py to norm_tools.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/qcDisplay.py to qcDisplay.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/stat_tools.py to stat_tools.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/tnseq_tools.py to tnseq_tools.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/transit_gui.py to transit_gui.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/transit_tools.py to transit_tools.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/trash.py to trash.cpython-39.pyc byte-compiling /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/pytransit/view_trash.py to view_trash.cpython-39.pyc running install_egg_info Copying tnseq_transit.egg-info to /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/lib/python3.9/dist-packages/tnseq_transit-3.2.1.egg-info Skipping SOURCES.txt running install_scripts Installing tpp script to /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/bin Installing transit script to /build/tnseq-transit-3.2.1/debian/tnseq-transit/usr/bin debian/rules override_dh_install make[1]: Entering directory '/build/tnseq-transit-3.2.1' dh_install mv debian/tnseq-transit/usr/bin/tpp debian/tnseq-transit/usr/bin/transit-tpp make[1]: Leaving directory '/build/tnseq-transit-3.2.1' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -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 'tnseq-transit' in '../tnseq-transit_3.2.1-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../tnseq-transit_3.2.1-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . 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/2123324/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2123324/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/2123324 and its subdirectories I: Current time: Wed Sep 4 11:57:07 +14 2024 I: pbuilder-time-stamp: 1725400627