Mon Aug 23 07:10:15 UTC 2021 I: starting to build tnseq-transit/bullseye/arm64 on jenkins on '2021-08-23 07:09' Mon Aug 23 07:10:15 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_14/26457/console.log Mon Aug 23 07:10:15 UTC 2021 I: Downloading source for bullseye/tnseq-transit=3.2.1-1 --2021-08-23 07:10:16-- http://cdn-fastly.deb.debian.org/debian/pool/main/t/tnseq-transit/tnseq-transit_3.2.1-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2219 (2.2K) Saving to: ‘tnseq-transit_3.2.1-1.dsc’ 0K .. 100% 85.5M=0s 2021-08-23 07:10:16 (85.5 MB/s) - ‘tnseq-transit_3.2.1-1.dsc’ saved [2219/2219] Mon Aug 23 07:10:16 UTC 2021 I: tnseq-transit_3.2.1-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: tnseq-transit Binary: tnseq-transit Architecture: any Version: 3.2.1-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Nilesh Patra Homepage: http://saclab.tamu.edu/essentiality/transit/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/tnseq-transit Vcs-Git: https://salsa.debian.org/med-team/tnseq-transit.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-python, python3-dev, python3-setuptools, python3-numpy, python3-scipy, python3-pil, python3-matplotlib, python3-statsmodels, python3-pubsub, bwa Package-List: tnseq-transit deb science optional arch=any Checksums-Sha1: 1928dc6256cdee7589d5d3d82d560517ac1210ce 26900130 tnseq-transit_3.2.1.orig.tar.gz 2b6d45ac6a071c5be87c1fe50af2f930f210995b 5792 tnseq-transit_3.2.1-1.debian.tar.xz Checksums-Sha256: e03908fd7ceea59d968a7814055b5d2cfcdceef82b2c1059de3527e2cef2b00f 26900130 tnseq-transit_3.2.1.orig.tar.gz b62e10030e84f1fcf1eb32521339ff6163bbfb3db40290ef5ba5dbdef006f4fc 5792 tnseq-transit_3.2.1-1.debian.tar.xz Files: 739e8fe747e24ff03f0a5626b250e423 26900130 tnseq-transit_3.2.1.orig.tar.gz a40abf4e322cef4c6b5b875bd7248fa6 5792 tnseq-transit_3.2.1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAl/k3kcUHG5wYXRyYTk3 NEBnbWFpbC5jb20ACgkQALrnSzQzafEijhAAi21c77f0hQILflnuNjDJDgfxsLtR DgxtKcCczG4h91vpxiZlrt5b4id98aZia9Qa0xVtM3Moxr3VSxV/Ncc/TY0AowBJ HsfWM3ziDOS10h0dkM3Lb5J4FluEqgavWDZFulFiTwH3M5m2imtkkIAA3N7HLEDj 3tXbRM3u5qbhQGBay0cw4wT38BViGAVR+MLrffDKCrgnSCuLrrnjaJVgpx26CzCJ Y0PQ+Z646CD++M0VLdsU3q4oUSr8yrVhNGkyMQxKWkkW59uzBIw0Uz8RCcvuBwxn aHGZ1F72hV6UIqIopM2L0xhRF65l8Fa3c23lW67r7BZ5B3ggVMsfklyBZ2XSiDDQ BLiJY316yd/AGdhUwvoec0FWmIk5kPJlaIa/LEOIxQNAa7LC9cpHDFs9lLXAWeUe B5Lq1Heds97r1nEnijUX6lXFKJuFPE7vTe/UxtulIhNI9WgSHQQxlzTz/+O/i+6b XbC6Sf4ZPwFywUQfvzin8/Rj/fq0GcNEFlzKQBUyJ9H/yIn+896SAgzH1BGXKNG8 2op8Dd7dssGRKi18UetNrlV9ppBEIHRStd/hAaLncKFyFGfCxtjZppPVoPtZF+r2 2gpgfq7WvDT2+axrm6j+1S84g3anBfO+7ySzlw71pdLNdnvn72EeNV0KzjnVNEky WiC8A2XRjOMsZcs= =Dntm -----END PGP SIGNATURE----- Mon Aug 23 07:10:16 UTC 2021 I: Checking whether the package is not for us Mon Aug 23 07:10:16 UTC 2021 I: Starting 1st build on remote node codethink12-arm64.debian.net. Mon Aug 23 07:10:16 UTC 2021 I: Preparing to do remote build '1' on codethink12-arm64.debian.net. Mon Aug 23 07:26:47 UTC 2021 I: Deleting $TMPDIR on codethink12-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Aug 22 19:10:23 -12 2021 I: pbuilder-time-stamp: 1629702623 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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.qrn4YDdd/trustedkeys.kbx': General error gpgv: Signature made Thu Dec 24 06:30:31 2020 -12 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/7433/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='7433' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.ZW9GtHDvIi/pbuilderrc_SWtT --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ZW9GtHDvIi/b1 --logfile b1/build.log tnseq-transit_3.2.1-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink12-arm64 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Aug 4 08:25 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Jul 28 07:09 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 93744 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Jul 28 07:09 more -rwsr-xr-x 1 root root 51360 Jul 28 07:09 mount -rwxr-xr-x 1 root root 14496 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 20 21:24 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Jul 28 07:09 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 30880 Jul 28 07:09 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Jul 28 07:09 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/7433/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-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 ... 19646 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-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 70.9 MB of archives. After unpacking 288 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-8 [142 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 mailcap all 3.69 [31.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 mime-support all 3.66 [10.9 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 bwa arm64 0.7.17-6+b1 [198 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 python3-distutils all 3.9.2-1 [143 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 fonts-lyx all 2.3.6-1 [205 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 libblas3 arm64 3.9.0-3 [101 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libmd0 arm64 1.0.3-3 [27.9 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libbsd0 arm64 0.11.3-1 [106 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 libexpat1-dev arm64 2.2.10-2 [126 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 libpng16-16 arm64 1.6.37-3 [289 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 libfreetype6 arm64 2.10.4+dfsg-1 [393 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 libgfortran5 arm64 10.2.1-6 [333 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 libimagequant0 arm64 2.12.2-1.1 [30.3 kB] Get: 61 http://deb.debian.org/debian bullseye/main arm64 libjbig0 arm64 2.1-3.1+b2 [27.8 kB] Get: 62 http://deb.debian.org/debian bullseye/main arm64 libjpeg62-turbo arm64 1:2.0.6-4 [133 kB] Get: 63 http://deb.debian.org/debian bullseye/main arm64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 64 http://deb.debian.org/debian bullseye/main arm64 libjs-jquery-ui all 1.12.1+dfsg-8 [232 kB] Get: 65 http://deb.debian.org/debian bullseye/main arm64 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 66 http://deb.debian.org/debian bullseye/main arm64 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 67 http://deb.debian.org/debian bullseye/main arm64 liblapack3 arm64 3.9.0-3 [1541 kB] Get: 68 http://deb.debian.org/debian bullseye/main arm64 liblbfgsb0 arm64 3.0+dfsg.3-9 [24.5 kB] Get: 69 http://deb.debian.org/debian bullseye/main arm64 liblcms2-2 arm64 2.12~rc1-2 [140 kB] Get: 70 http://deb.debian.org/debian bullseye/main arm64 libpython3.9 arm64 3.9.2-1 [1556 kB] Get: 71 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-dev arm64 3.9.2-1 [3835 kB] Get: 72 http://deb.debian.org/debian bullseye/main arm64 libpython3-dev arm64 3.9.2-3 [21.7 kB] Get: 73 http://deb.debian.org/debian bullseye/main arm64 libwebp6 arm64 0.6.1-2.1 [244 kB] Get: 74 http://deb.debian.org/debian bullseye/main arm64 libtiff5 arm64 4.2.0-1 [276 kB] Get: 75 http://deb.debian.org/debian bullseye/main arm64 libwebpdemux2 arm64 0.6.1-2.1 [87.5 kB] Get: 76 http://deb.debian.org/debian bullseye/main arm64 libwebpmux3 arm64 0.6.1-2.1 [96.7 kB] Get: 77 http://deb.debian.org/debian bullseye/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 78 http://deb.debian.org/debian bullseye/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 79 http://deb.debian.org/debian bullseye/main arm64 libxcb1 arm64 1.14-3 [138 kB] Get: 80 http://deb.debian.org/debian bullseye/main arm64 ttf-bitstream-vera all 1.10-8.1 [223 kB] Get: 81 http://deb.debian.org/debian bullseye/main arm64 python-matplotlib-data all 3.3.4-1 [4153 kB] Get: 82 http://deb.debian.org/debian bullseye/main arm64 python3-six all 1.16.0-2 [17.5 kB] Get: 83 http://deb.debian.org/debian bullseye/main arm64 python3-cycler all 0.10.0-3 [8084 B] Get: 84 http://deb.debian.org/debian bullseye/main arm64 python3-dateutil all 2.8.1-6 [79.2 kB] Get: 85 http://deb.debian.org/debian bullseye/main arm64 python3-decorator all 4.4.2-2 [15.8 kB] Get: 86 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 87 http://deb.debian.org/debian bullseye/main arm64 python3.9-dev arm64 3.9.2-1 [515 kB] Get: 88 http://deb.debian.org/debian bullseye/main arm64 python3-dev arm64 3.9.2-3 [24.8 kB] Get: 89 http://deb.debian.org/debian bullseye/main arm64 python3-kiwisolver arm64 1.3.1-1+b1 [51.6 kB] Get: 90 http://deb.debian.org/debian bullseye/main arm64 python3-pyparsing all 2.4.7-1 [109 kB] Get: 91 http://deb.debian.org/debian bullseye/main arm64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 92 http://deb.debian.org/debian bullseye/main arm64 python3-numpy arm64 1:1.19.5-1 [3196 kB] Get: 93 http://deb.debian.org/debian bullseye/main arm64 python3-pil arm64 8.1.2+dfsg-0.3 [428 kB] Get: 94 http://deb.debian.org/debian bullseye/main arm64 python3-matplotlib arm64 3.3.4-1 [4109 kB] Get: 95 http://deb.debian.org/debian bullseye/main arm64 python3-tz all 2021.1-1 [34.8 kB] Get: 96 http://deb.debian.org/debian bullseye/main arm64 python3-pandas-lib arm64 1.1.5+dfsg-2 [2914 kB] Get: 97 http://deb.debian.org/debian bullseye/main arm64 python3-pandas all 1.1.5+dfsg-2 [2096 kB] Get: 98 http://deb.debian.org/debian bullseye/main arm64 python3-patsy all 0.5.1-3 [172 kB] Get: 99 http://deb.debian.org/debian bullseye/main arm64 python3-pubsub all 4.0.3-4 [46.6 kB] Get: 100 http://deb.debian.org/debian bullseye/main arm64 python3-scipy arm64 1.6.0-2 [11.6 MB] Get: 101 http://deb.debian.org/debian bullseye/main arm64 python3-setuptools all 52.0.0-4 [366 kB] Get: 102 http://deb.debian.org/debian bullseye/main arm64 python3-statsmodels-lib arm64 0.12.2-1 [1204 kB] Get: 103 http://deb.debian.org/debian bullseye/main arm64 python3-statsmodels all 0.12.2-1 [4455 kB] Fetched 70.9 MB in 2s (37.7 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 ... 19646 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_arm64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../3-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:arm64. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_arm64.deb ... Unpacking libpython3.9-minimal:arm64 (3.9.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../6-libexpat1_2.2.10-2_arm64.deb ... Unpacking libexpat1:arm64 (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_arm64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:arm64 (3.9.2-1) ... Setting up libexpat1:arm64 (2.2.10-2) ... 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 ... 20513 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_arm64.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 ... Unpacking media-types (4.0.0) ... Selecting previously unselected package mailcap. 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Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.9.2-3_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20958 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_arm64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../03-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../06-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. 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Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../20-libelf1_0.183-1_arm64.deb ... Unpacking libelf1:arm64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../21-dwz_0.13+20210201-1_arm64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:arm64. Preparing to unpack .../22-libicu67_67.1-7_arm64.deb ... Unpacking libicu67:arm64 (67.1-7) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../23-libxml2_2.9.10+dfsg-6.7_arm64.deb ... Unpacking libxml2:arm64 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../24-gettext_0.21-4_arm64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../25-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... 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Preparing to unpack .../32-libblas3_3.9.0-3_arm64.deb ... Unpacking libblas3:arm64 (3.9.0-3) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../33-libbrotli1_1.0.9-2+b2_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b2) ... Selecting previously unselected package libmd0:arm64. Preparing to unpack .../34-libmd0_1.0.3-3_arm64.deb ... Unpacking libmd0:arm64 (1.0.3-3) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../35-libbsd0_0.11.3-1_arm64.deb ... Unpacking libbsd0:arm64 (0.11.3-1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../36-libdeflate0_1.7-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.7-1) ... Selecting previously unselected package libexpat1-dev:arm64. Preparing to unpack .../37-libexpat1-dev_2.2.10-2_arm64.deb ... Unpacking libexpat1-dev:arm64 (2.2.10-2) ... Selecting previously unselected package libpng16-16:arm64. Preparing to unpack .../38-libpng16-16_1.6.37-3_arm64.deb ... Unpacking libpng16-16:arm64 (1.6.37-3) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../39-libfreetype6_2.10.4+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (2.10.4+dfsg-1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../40-libgfortran5_10.2.1-6_arm64.deb ... Unpacking libgfortran5:arm64 (10.2.1-6) ... Selecting previously unselected package libimagequant0:arm64. Preparing to unpack .../41-libimagequant0_2.12.2-1.1_arm64.deb ... Unpacking libimagequant0:arm64 (2.12.2-1.1) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../42-libjbig0_2.1-3.1+b2_arm64.deb ... Unpacking libjbig0:arm64 (2.1-3.1+b2) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../43-libjpeg62-turbo_1%3a2.0.6-4_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.0.6-4) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../44-libjs-jquery_3.5.1+dfsg+~3.5.5-7_all.deb ... Unpacking libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../45-libjs-jquery-ui_1.12.1+dfsg-8_all.deb ... Unpacking libjs-jquery-ui (1.12.1+dfsg-8) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../46-libjs-underscore_1.9.1~dfsg-3_all.deb ... Unpacking libjs-underscore (1.9.1~dfsg-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../47-libjs-sphinxdoc_3.4.3-2_all.deb ... Unpacking libjs-sphinxdoc (3.4.3-2) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../48-liblapack3_3.9.0-3_arm64.deb ... Unpacking liblapack3:arm64 (3.9.0-3) ... Selecting previously unselected package liblbfgsb0:arm64. Preparing to unpack .../49-liblbfgsb0_3.0+dfsg.3-9_arm64.deb ... Unpacking liblbfgsb0:arm64 (3.0+dfsg.3-9) ... Selecting previously unselected package liblcms2-2:arm64. Preparing to unpack .../50-liblcms2-2_2.12~rc1-2_arm64.deb ... Unpacking liblcms2-2:arm64 (2.12~rc1-2) ... Selecting previously unselected package libpython3.9:arm64. Preparing to unpack .../51-libpython3.9_3.9.2-1_arm64.deb ... Unpacking libpython3.9:arm64 (3.9.2-1) ... Selecting previously unselected package libpython3.9-dev:arm64. Preparing to unpack .../52-libpython3.9-dev_3.9.2-1_arm64.deb ... Unpacking libpython3.9-dev:arm64 (3.9.2-1) ... Selecting previously unselected package libpython3-dev:arm64. Preparing to unpack .../53-libpython3-dev_3.9.2-3_arm64.deb ... Unpacking libpython3-dev:arm64 (3.9.2-3) ... Selecting previously unselected package libwebp6:arm64. Preparing to unpack .../54-libwebp6_0.6.1-2.1_arm64.deb ... Unpacking libwebp6:arm64 (0.6.1-2.1) ... Selecting previously unselected package libtiff5:arm64. Preparing to unpack .../55-libtiff5_4.2.0-1_arm64.deb ... 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Unpacking python3-statsmodels (0.12.2-1) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:arm64 (1.5.3-1) ... Setting up liblcms2-2:arm64 (2.12~rc1-2) ... Setting up libxau6:arm64 (1:1.0.9-1) ... Setting up ttf-bitstream-vera (1.10-8.1) ... Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:arm64 (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:arm64 (1.0.9-2+b2) ... Setting up libmagic1:arm64 (1:5.39-3) ... Setting up libdeflate0:arm64 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libjbig0:arm64 (2.1-3.1+b2) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:arm64 (3.9.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libexpat1-dev:arm64 (2.2.10-2) ... Setting up libjpeg62-turbo:arm64 (1:2.0.6-4) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up libimagequant0:arm64 (2.12.2-1.1) ... Setting up libpng16-16:arm64 (1.6.37-3) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:arm64 (0.6.1-2.1) ... Setting up libgfortran5:arm64 (10.2.1-6) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up libmd0:arm64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libmpdec3:arm64 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libtiff5:arm64 (4.2.0-1) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up python-matplotlib-data (3.3.4-1) ... Setting up libwebpmux3:arm64 (0.6.1-2.1) ... Setting up libbsd0:arm64 (0.11.3-1) ... Setting up mailcap (3.69) ... Setting up libelf1:arm64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3) ... Setting up liblapack3:arm64 (3.9.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (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:arm64 (0.6.1-2.1) ... Setting up libreadline8:arm64 (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) ... Setting up libfreetype6:arm64 (2.10.4+dfsg-1) ... 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:arm64 (3.9.2-1) ... Setting up libpython3-stdlib:arm64 (3.9.2-3) ... Setting up liblbfgsb0:arm64 (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:arm64 (3.9.2-1) ... Setting up python3.9 (3.9.2-1) ... Setting up libpython3.9-dev:arm64 (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:arm64 (8.1.2+dfsg-0.3) ... 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:arm64 (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:arm64 (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:arm64 (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) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/tnseq-transit-3.2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../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 arm64 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-arm64' 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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Running Binomial Method... 38.0% [binomial] Running Binomial Method... 38.1% [binomial] Running Binomial Method... 38.2% [binomial] Running Binomial Method... 38.3% [binomial] Running Binomial Method... 38.4% [binomial] Running Binomial Method... 38.5% [binomial] Running Binomial Method... 38.5% [binomial] Running Binomial Method... 38.6% [binomial] Running Binomial Method... 38.7% [binomial] Running Binomial Method... 38.8% [binomial] Running Binomial Method... 38.9% [binomial] Running Binomial Method... 39.0% [binomial] Running Binomial Method... 39.1% [binomial] Running Binomial Method... 39.2% [binomial] Running Binomial Method... 39.3% [binomial] Running Binomial Method... 39.4% [binomial] Running Binomial Method... 39.5% [binomial] Running Binomial Method... 39.5% [binomial] Running Binomial Method... 39.6% [binomial] Running Binomial Method... 39.7% [binomial] Running Binomial Method... 39.8% [binomial] Running Binomial Method... 39.9% [binomial] Running Binomial Method... 40.0% 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Method... 60.6% [binomial] Running Binomial Method... 60.7% [binomial] Running Binomial Method... 60.8% [binomial] Running Binomial Method... 60.9% [binomial] Running Binomial Method... 61.0% [binomial] Running Binomial Method... 61.1% [binomial] Running Binomial Method... 61.2% [binomial] Running Binomial Method... 61.3% [binomial] Running Binomial Method... 61.4% [binomial] Running Binomial Method... 61.5% [binomial] Running Binomial Method... 61.5% [binomial] Running Binomial Method... 61.6% [binomial] Running Binomial Method... 61.7% [binomial] Running Binomial Method... 61.8% [binomial] Running Binomial Method... 61.9% [binomial] Running Binomial Method... 62.0% [binomial] Running Binomial Method... 62.1% [binomial] Running Binomial Method... 62.2% [binomial] Running Binomial Method... 62.3% [binomial] Running Binomial Method... 62.4% [binomial] Running Binomial Method... 62.5% [binomial] Running Binomial Method... 62.5% [binomial] Running Binomial Method... 62.6% [binomial] Running Binomial Method... 62.7% [binomial] Running Binomial Method... 62.8% [binomial] Running Binomial Method... 62.9% [binomial] Running Binomial Method... 63.0% [binomial] Running Binomial Method... 63.1% [binomial] Running Binomial Method... 63.2% [binomial] Running Binomial Method... 63.3% [binomial] Running Binomial Method... 63.4% [binomial] Running Binomial Method... 63.5% [binomial] Running Binomial Method... 63.5% [binomial] Running Binomial Method... 63.6% [binomial] Running Binomial Method... 63.7% [binomial] Running Binomial Method... 63.8% [binomial] Running Binomial Method... 63.9% [binomial] Running Binomial Method... 64.0% [binomial] Running Binomial Method... 64.1% [binomial] Running Binomial Method... 64.2% [binomial] Running Binomial Method... 64.3% [binomial] Running Binomial Method... 64.4% [binomial] Running Binomial Method... 64.5% [binomial] Running Binomial Method... 64.5% [binomial] Running Binomial Method... 64.6% [binomial] Running Binomial Method... 64.7% 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Running Binomial Method... 68.9% [binomial] Running Binomial Method... 69.0% [binomial] Running Binomial Method... 69.1% [binomial] Running Binomial Method... 69.2% [binomial] Running Binomial Method... 69.3% [binomial] Running Binomial Method... 69.4% [binomial] Running Binomial Method... 69.5% [binomial] Running Binomial Method... 69.5% [binomial] Running Binomial Method... 69.6% [binomial] Running Binomial Method... 69.7% [binomial] Running Binomial Method... 69.8% [binomial] Running Binomial Method... 69.9% [binomial] Running Binomial Method... 70.0% [binomial] Running Binomial Method... 70.1% [binomial] Running Binomial Method... 70.2% [binomial] Running Binomial Method... 70.3% [binomial] Running Binomial Method... 70.4% [binomial] Running Binomial Method... 70.5% [binomial] Running Binomial Method... 70.5% [binomial] Running Binomial Method... 70.6% [binomial] Running Binomial Method... 70.7% [binomial] Running Binomial Method... 70.8% [binomial] Running Binomial Method... 70.9% 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Running Binomial Method... 75.1% [binomial] Running Binomial Method... 75.2% [binomial] Running Binomial Method... 75.3% [binomial] Running Binomial Method... 75.4% [binomial] Running Binomial Method... 75.5% [binomial] Running Binomial Method... 75.5% [binomial] Running Binomial Method... 75.6% [binomial] Running Binomial Method... 75.7% [binomial] Running Binomial Method... 75.8% [binomial] Running Binomial Method... 75.9% [binomial] Running Binomial Method... 76.0% [binomial] Running Binomial Method... 76.1% [binomial] Running Binomial Method... 76.2% [binomial] Running Binomial Method... 76.3% [binomial] Running Binomial Method... 76.4% [binomial] Running Binomial Method... 76.5% [binomial] Running Binomial Method... 76.5% [binomial] Running Binomial Method... 76.6% [binomial] Running Binomial Method... 76.7% [binomial] Running Binomial Method... 76.8% [binomial] Running Binomial Method... 76.9% [binomial] Running Binomial Method... 77.0% [binomial] Running Binomial Method... 77.1% 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Method... 79.2% [binomial] Running Binomial Method... 79.3% [binomial] Running Binomial Method... 79.4% [binomial] Running Binomial Method... 79.5% [binomial] Running Binomial Method... 79.5% [binomial] Running Binomial Method... 79.6% [binomial] Running Binomial Method... 79.7% [binomial] Running Binomial Method... 79.8% [binomial] Running Binomial Method... 79.9% [binomial] Running Binomial Method... 80.0% [binomial] Running Binomial Method... 80.1% [binomial] Running Binomial Method... 80.2% [binomial] Running Binomial Method... 80.3% [binomial] Running Binomial Method... 80.4% [binomial] Running Binomial Method... 80.5% [binomial] Running Binomial Method... 80.5% [binomial] Running Binomial Method... 80.6% [binomial] Running Binomial Method... 80.7% [binomial] Running Binomial Method... 80.8% [binomial] Running Binomial Method... 80.9% [binomial] Running Binomial Method... 81.0% [binomial] Running Binomial Method... 81.1% [binomial] Running Binomial Method... 81.2% [binomial] Running Binomial Method... 81.3% [binomial] Running Binomial Method... 81.4% [binomial] Running Binomial Method... 81.5% [binomial] Running Binomial Method... 81.5% [binomial] Running Binomial Method... 81.6% [binomial] Running Binomial Method... 81.7% [binomial] Running Binomial Method... 81.8% [binomial] Running Binomial Method... 81.9% [binomial] Running Binomial Method... 82.0% [binomial] Running Binomial Method... 82.1% [binomial] Running Binomial Method... 82.2% [binomial] Running Binomial Method... 82.3% [binomial] Running Binomial Method... 82.4% [binomial] Running Binomial Method... 82.5% [binomial] Running Binomial Method... 82.5% [binomial] Running Binomial Method... 82.6% [binomial] Running Binomial Method... 82.7% [binomial] Running Binomial Method... 82.8% [binomial] Running Binomial Method... 82.9% [binomial] Running Binomial Method... 83.0% [binomial] Running Binomial Method... 83.1% [binomial] Running Binomial Method... 83.2% [binomial] Running Binomial Method... 83.3% 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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... 95.0% [gumbel] Running Gumbel Method... 95.1% [gumbel] Running Gumbel Method... 95.2% [gumbel] Running Gumbel Method... 95.3% [gumbel] Running Gumbel Method... 95.4% [gumbel] Running Gumbel Method... 95.5% [gumbel] Running Gumbel Method... 95.5% [gumbel] Running Gumbel Method... 95.6% [gumbel] Running Gumbel Method... 95.7% [gumbel] Running Gumbel Method... 95.8% [gumbel] Running Gumbel Method... 95.9% [gumbel] Running Gumbel Method... 96.0% [gumbel] Running Gumbel Method... 96.1% [gumbel] Running Gumbel Method... 96.2% [gumbel] Running Gumbel Method... 96.3% [gumbel] Running Gumbel Method... 96.4% [gumbel] Running Gumbel Method... 96.5% [gumbel] Running Gumbel Method... 96.5% [gumbel] Running Gumbel Method... 96.6% [gumbel] Running Gumbel Method... 96.7% [gumbel] Running Gumbel Method... 96.8% [gumbel] Running Gumbel Method... 96.9% [gumbel] Running Gumbel Method... 97.0% [gumbel] Running Gumbel Method... 97.1% [gumbel] Running Gumbel Method... 97.2% [gumbel] Running Gumbel 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: 1.7s 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 36 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... 0.10 sec' b'[bwa_index] Construct BWT for the packed sequence...' b'[bwa_index] 7.73 seconds elapse.' b'[bwa_index] Update BWT... 0.06 sec' b'[bwa_index] Pack forward-only FASTA... 0.08 sec' b'[bwa_index] Construct SA from BWT and Occ... 2.59 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: 10.582 sec; CPU: 10.575 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 0.504 CPU sec, 0.584 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: 0.617 sec; CPU: 0.536 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 0.513 CPU sec, 0.529 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: 0.553 sec; CPU: 0.546 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 742.520s 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: 08/22/2021 19:24:33 # 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: 08/22/2021 19:24:39 # 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_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../tnseq-transit_3.2.1-1_arm64.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: 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/7433 and its subdirectories I: Current time: Sun Aug 22 19:26:43 -12 2021 I: pbuilder-time-stamp: 1629703603 Mon Aug 23 07:26:48 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink11-arm64.debian.net. Mon Aug 23 07:26:48 UTC 2021 I: Preparing to do remote build '2' on codethink11-arm64.debian.net. Mon Aug 23 07:43:42 UTC 2021 I: Deleting $TMPDIR on codethink11-arm64.debian.net. Mon Aug 23 07:43:43 UTC 2021 I: tnseq-transit_3.2.1-1_arm64.changes: Format: 1.8 Date: Thu, 24 Dec 2020 23:44:18 +0530 Source: tnseq-transit Binary: tnseq-transit Architecture: arm64 Version: 3.2.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: tnseq-transit - statistical calculations of essentiality of genes or genomic regi Changes: tnseq-transit (3.2.1-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.5.1 (routine-update) Checksums-Sha1: 01b6730df1f52fd4597647cf6878ba436a22f8d0 6792 tnseq-transit_3.2.1-1_arm64.buildinfo c8d452061eb5bea958879692e46d2cf9cb313c73 8954788 tnseq-transit_3.2.1-1_arm64.deb Checksums-Sha256: 038a4e65461ad9678cd44eb03600ae3d216b9331829c132ffb37644efd263346 6792 tnseq-transit_3.2.1-1_arm64.buildinfo e802e88d1836da8843269953deaf8e2ea6e3a464680ac89b2736ae80e0a3fe3b 8954788 tnseq-transit_3.2.1-1_arm64.deb Files: 9c01e6cbc3217ba48cb266cc06f02ff1 6792 science optional tnseq-transit_3.2.1-1_arm64.buildinfo 06db7e60e8371885bc4aa25d88b75f58 8954788 science optional tnseq-transit_3.2.1-1_arm64.deb Mon Aug 23 07:43:44 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.ZW9GtHDvIi/tnseq-transit_3.2.1-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.ZW9GtHDvIi/tnseq-transit_3.2.1-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.ZW9GtHDvIi/tnseq-transit_3.2.1-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.ZW9GtHDvIi/b1/tnseq-transit_3.2.1-1_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.ZW9GtHDvIi/b2/tnseq-transit_3.2.1-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.501s) 0.500s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.127s) 0.127s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Aug 23 07:43:45 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Mon Aug 23 07:43:45 UTC 2021 I: tnseq-transit from bullseye built successfully and reproducibly on arm64. Mon Aug 23 07:43:47 UTC 2021 I: Submitting .buildinfo files to external archives: Mon Aug 23 07:43:47 UTC 2021 I: Submitting 8.0K b1/tnseq-transit_3.2.1-1_arm64.buildinfo.asc Mon Aug 23 07:43:49 UTC 2021 I: Submitting 8.0K b2/tnseq-transit_3.2.1-1_arm64.buildinfo.asc Mon Aug 23 07:43:50 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Aug 23 07:43:50 UTC 2021 I: Done submitting .buildinfo files. Mon Aug 23 07:43:50 UTC 2021 I: Removing signed tnseq-transit_3.2.1-1_arm64.buildinfo.asc files: removed './b1/tnseq-transit_3.2.1-1_arm64.buildinfo.asc' removed './b2/tnseq-transit_3.2.1-1_arm64.buildinfo.asc'