Thu Feb 6 10:29:07 UTC 2025 I: starting to build tnseq-transit/trixie/arm64 on jenkins on '2025-02-06 10:28' Thu Feb 6 10:29:07 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_8/48013/console.log Thu Feb 6 10:29:07 UTC 2025 I: Downloading source for trixie/tnseq-transit=3.3.12-1 --2025-02-06 10:29:08-- http://deb.debian.org/debian/pool/main/t/tnseq-transit/tnseq-transit_3.3.12-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2264 (2.2K) [text/prs.lines.tag] Saving to: ‘tnseq-transit_3.3.12-1.dsc’ 0K .. 100% 381M=0s 2025-02-06 10:29:08 (381 MB/s) - ‘tnseq-transit_3.3.12-1.dsc’ saved [2264/2264] Thu Feb 6 10:29:08 UTC 2025 I: tnseq-transit_3.3.12-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: tnseq-transit Binary: tnseq-transit Architecture: any Version: 3.3.12-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: http://saclab.tamu.edu/essentiality/transit/ Standards-Version: 4.7.0 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-sequence-python3, python3-dev, python3-setuptools, python3-numpy, python3-scipy, python3-pil, python3-matplotlib, python3-sklearn , python3-statsmodels, python3-pubsub, bwa Package-List: tnseq-transit deb science optional arch=any Checksums-Sha1: b080fa2fbfbe0999129f36c06b17600a0d04f893 39516308 tnseq-transit_3.3.12.orig.tar.gz 158271580191895ee83d2fe92bbec51a3394a586 7652 tnseq-transit_3.3.12-1.debian.tar.xz Checksums-Sha256: 26df50e08f6fca0d5081f762a9312f72b67815e82bd6ddc51a056ecda84c4bbd 39516308 tnseq-transit_3.3.12.orig.tar.gz 0bc0395f91ebcc2fd1ac6927e11099ce129e123c784602cd7027d6da876afc5c 7652 tnseq-transit_3.3.12-1.debian.tar.xz Files: 32466b71fcab11429c39606024cecb6a 39516308 tnseq-transit_3.3.12.orig.tar.gz 94d5b885ed06405875c32af95ee8d06e 7652 tnseq-transit_3.3.12-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEEj23hBDd/OxHnQXSHMfMURUShdBoFAmeg5hIRHHRjaGV0QGRl Ymlhbi5vcmcACgkQMfMURUShdBqT4Q/+K9tIt5QNWdRSA6/yFWnsLlOmH2UpqW90 2AdkhSJMq4t/o4a/l1WbyRNIRDTf/oX0NrLPMqO/EvceVJsrr29Bl+FWvypPt3jZ qASXE61eWYyw8T5jwKaIomUqahp40p6IKF89o/2PRi8Vtj6fFyyTpgfeSzuw1riz To32hlO8sV3W1vrZFwe5xh+PGHRZmsRRJKpeNf6jBK8/hWpHrn6GbumODjLnq9av +wrBSB/cmuiFiyoqbfXSBMlCfwfkfq2hxg1+s1YECH9CN19DcjwwQYZYDGvOOM9q dE5/EH2INYHpQ1ryYL5CjraYU+SeEaD2HvptjBxS720ngfBP9Jw13LMKIn/BgIAE hhNc2QkbvEljx/EDq9kJdj60VJ6brE4Ta+9aSfPtLA//Ei/bq57cUaejniODDj2M kP8Pt32sVGaaTJaAqPhS71FHB2xL0949KxKx7lNHB5edOkA/+u4/paIsU+4K6XgT lPRi1Kp4aIlOuoW2lomKRGvvzW5/8XmeOxjLKNjwfQbuypvmbxpq3tO116kzUTfF EFTMbhCPd+SZjLaZqcvtziHxNla0TMQpbmTDCnPXKkgKEyTFWzHPCg6LzB775l0J n3aRGk+UUJQCW46Dedy5QB7QYZZ5VlB3getKlJZVEzH4Q4tf070PcaK2TekZfDM7 UDPMcHqiy1Q= =yw8U -----END PGP SIGNATURE----- Thu Feb 6 10:29:08 UTC 2025 I: Checking whether the package is not for us Thu Feb 6 10:29:08 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Thu Feb 6 10:29:08 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Thu Feb 6 10:33:05 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Feb 5 22:29:10 -12 2025 I: pbuilder-time-stamp: 1738837750 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [tnseq-transit_3.3.12-1.dsc] I: copying [./tnseq-transit_3.3.12.orig.tar.gz] I: copying [./tnseq-transit_3.3.12-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./tnseq-transit_3.3.12-1.dsc: unsupported subcommand dpkg-source: info: extracting tnseq-transit in tnseq-transit-3.3.12 dpkg-source: info: unpacking tnseq-transit_3.3.12.orig.tar.gz dpkg-source: info: unpacking tnseq-transit_3.3.12-1.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 dpkg-source: info: applying fix_problematic_comparison.patch dpkg-source: info: applying remove_pkg_resources.patch dpkg-source: info: applying repair.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1206982/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='352bd7fe9e11437681a2d97e539bcc52' 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='1206982' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.zKecEb8X/pbuilderrc_CaSE --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.zKecEb8X/b1 --logfile b1/build.log tnseq-transit_3.3.12-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1206982/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-dev, python3-setuptools, python3-numpy, python3-scipy, python3-pil, python3-matplotlib, python3-sklearn, 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 ... 19957 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-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-sklearn; however: Package python3-sklearn 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} blt{a} bsdextrautils{a} bwa{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lyx{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgcrypt20{a} libgfortran5{a} libglib2.0-0t64{a} libgpg-error0{a} libgraphite2-3{a} libharfbuzz0b{a} libicu72{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} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libopenjp2-7{a} libpipeline1{a} libpng16-16t64{a} libproc2-0{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-attr{a} python3-autocommand{a} python3-brotli{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-fonttools{a} python3-fs{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-joblib{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-patsy{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pubsub{a} python3-pyparsing{a} python3-scipy{a} python3-setuptools{a} python3-sklearn{a} python3-sklearn-lib{a} python3-statsmodels{a} python3-statsmodels-lib{a} python3-sympy{a} python3-threadpoolctl{a} python3-tk{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-unicodedata2{a} python3-zipp{a} python3.12-tk{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} readline-common{a} sensible-utils{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} x11-common{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl isympy-common javascript-common libarchive-cpio-perl libglib2.0-data libgpg-error-l10n libltdl-dev libmail-sendmail-perl linux-sysctl-defaults lynx psmisc python3-bottleneck python3-bs4 python3-colorama python3-cssselect python3-cvxopt python3-html5lib python3-jinja2 python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pooch python3-psutil python3-pytest python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 156 newly installed, 0 to remove and 0 not upgraded. Need to get 125 MB of archives. After unpacking 631 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.13-minimal arm64 3.13.1-3+b1 [852 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.13-minimal arm64 3.13.1-3+b1 [1987 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.13.1-2 [27.0 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-6 [257 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libpython3.13-stdlib arm64 3.13.1-3+b1 [1913 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 python3.13 arm64 3.13.1-3+b1 [740 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B] Get: 14 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.13.1-2 [28.0 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-7 [62.4 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-7 [868 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-2 [91.5 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [984 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.44-3 [273 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-2 [317 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-2 [386 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b4 [27.2 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libxft2 arm64 2.3.6-1+b4 [51.6 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+24 [217 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libxss1 arm64 1:1.2.3-1+b3 [17.1 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libtk8.6 arm64 8.6.16-1 [741 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7+b1 [538 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 blt arm64 2.5.3+dfsg-7+b1 [6344 B] Get: 53 http://deb.debian.org/debian trixie/main arm64 bwa arm64 0.7.18-1 [198 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-2 [539 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 60 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 75 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 75.6.0-1 [720 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20250108 [113 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 fonts-lyx all 2.4.3-1 [190 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.1-2 [104 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libgpg-error0 arm64 1.51-3 [78.5 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-12 [361 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.82.4-2 [1413 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 10.2.0-1 [443 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b2 [25.6 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libopenjp2-7 arm64 2.5.0-2+b4 [185 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libpython3.13 arm64 3.13.1-3+b1 [1970 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libpython3.13-dev arm64 3.13.1-3+b1 [4682 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libpython3-dev arm64 3.13.1-2 [10.2 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libqhull-r8.0 arm64 2020.2-6+b2 [229 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libraqm0 arm64 0.10.2-1 [13.6 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [113 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libwebpmux3 arm64 1.5.0-0.1 [125 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libxslt1.1 arm64 1.1.35-1.1+b1 [222 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 python3-attr all 24.3.0-1 [68.8 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 python3-brotli arm64 1.1.0-2+b6 [306 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [3815 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 python3-contourpy arm64 1.3.1-1 [237 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 python3-cycler all 0.12.1-1 [9496 B] Get: 122 http://deb.debian.org/debian trixie/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 python3.13-dev arm64 3.13.1-3+b1 [504 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 python3-dev arm64 3.13.1-2 [26.1 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 python3-tz all 2024.2-1 [31.0 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 python3-fs all 2.4.16-6 [95.1 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 python3-lxml arm64 5.3.0-1+b1 [1433 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 python3-lz4 arm64 4.4.0+dfsg-1 [25.6 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 python3-scipy arm64 1.14.1-4 [18.5 MB] Get: 132 http://deb.debian.org/debian trixie/main arm64 python3-mpmath all 1.3.0-1 [419 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 python3-sympy all 1.13.3-1 [4147 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 python3-unicodedata2 arm64 15.1.0+ds-1+b4 [298 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 unicode-data all 15.1.0-1 [8547 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 python3-fonttools arm64 4.55.3-2 [1501 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 python3-joblib all 1.3.2-6 [216 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 python3-kiwisolver arm64 1.4.7-3 [71.5 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 python3-pil arm64 10.4.0-1.1 [498 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 python3.12-tk arm64 3.12.8-5+b1 [111 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 python3.13-tk arm64 3.13.1-3+b1 [102 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 python3-tk arm64 3.13.1-1 [9464 B] Get: 144 http://deb.debian.org/debian trixie/main arm64 python3-pil.imagetk arm64 10.4.0-1.1 [79.7 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 python3-matplotlib arm64 3.8.3-3+b2 [5583 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-7 [6029 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 python3-pandas all 2.2.3+dfsg-7 [3097 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 python3-patsy all 1.0.1-1 [172 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 python3-pubsub all 4.0.3-7 [46.7 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 python3-sklearn-lib arm64 1.4.2+dfsg-7+b1 [5397 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 python3-sklearn all 1.4.2+dfsg-7 [2248 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 python3-statsmodels-lib arm64 0.14.4+dfsg-1+b2 [2077 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 python3-statsmodels all 0.14.4+dfsg-1 [4825 kB] Fetched 125 MB in 0s (252 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19957 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.1-3+b1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.1-3+b1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.1-3+b1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.1-3+b1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.1-3+b1_arm64.deb ... Unpacking python3.13 (3.13.1-3+b1) ... 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Setting up libblas3:arm64 (3.12.1-2) ... 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 (2.6.4-1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libfribidi0:arm64 (1.0.16-1) ... Setting up libimagequant0:arm64 (2.18.0-1+b2) ... Setting up libproc2-0:arm64 (2:4.0.4-7) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-3) ... Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... Setting up autopoint (0.23.1-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libgfortran5:arm64 (14.2.0-12) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:arm64 (1.5.0-0.1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.6-1) ... Setting up dwz (0.15-1+b1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/tnseq-transit-3.3.12/ && 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_3.3.12-1_source.changes dpkg-buildpackage: info: source package tnseq-transit dpkg-buildpackage: info: source version 3.3.12-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Detiste dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean running clean removing '/build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/tnseq-transit-3.3.12' rm -rf tests_invalid_data rm -rf tnseq_transit.egg-info make[1]: Leaving directory '/build/reproducible-path/tnseq-transit-3.3.12' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/tnseq-transit-3.3.12' mkdir -p tests_invalid_data if [ -L tests/H37Rv.fna ] && ! [ -e tests/H37Rv.fna ] \ ; then mv tests/H37Rv.fna tests_invalid_data \ ; fi dh_auto_configure I: pybuild base:311: python3.13 setup.py config running config make[1]: Leaving directory '/build/reproducible-path/tnseq-transit-3.3.12' dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/generic_tools copying src/pytransit/generic_tools/file_system_py.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/generic_tools copying src/pytransit/generic_tools/__init__.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/generic_tools creating /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytpp copying src/pytpp/tpp_tools.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytpp copying src/pytpp/tpp_gui.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytpp copying src/pytpp/__main__.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytpp copying src/pytpp/__init__.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytpp copying src/pytransit/view_trash.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit copying src/pytransit/trash.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit copying src/pytransit/transit_tools.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit copying src/pytransit/transit_gui.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit copying src/pytransit/tnseq_tools.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit copying src/pytransit/stat_tools.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit copying src/pytransit/qcDisplay.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit copying src/pytransit/norm_tools.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit copying src/pytransit/images.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit copying src/pytransit/fileDisplay.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit copying src/pytransit/draw_trash.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit copying src/pytransit/__main__.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit copying src/pytransit/__init__.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit creating /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/zinb.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/utest.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/ttnfitness.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/tnseq_stats.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/tn5gaps.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/resampling.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/rankproduct.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/pathway_enrichment.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/normalize.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/norm.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/hmm.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/heatmap.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/gumbel.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/griffin.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/gi.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/example.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/corrplot.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/binomial.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/base.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/anova.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/__init__.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis copying src/pytransit/analysis/CGI.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis creating /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/export copying src/pytransit/export/prot_table.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/export copying src/pytransit/export/mean_counts.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/export copying src/pytransit/export/igv.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/export copying src/pytransit/export/combined_wig.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/export copying src/pytransit/export/base.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/export copying src/pytransit/export/__init__.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/export creating /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/convert copying src/pytransit/convert/gff_to_prot_table.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/convert copying src/pytransit/convert/base.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/convert copying src/pytransit/convert/__init__.py -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/convert running egg_info creating transit1.egg-info writing transit1.egg-info/PKG-INFO writing dependency_links to transit1.egg-info/dependency_links.txt writing entry points to transit1.egg-info/entry_points.txt writing requirements to transit1.egg-info/requires.txt writing top-level names to transit1.egg-info/top_level.txt writing manifest file 'transit1.egg-info/SOURCES.txt' reading manifest file 'transit1.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' adding license file 'LICENSE.md' writing manifest file 'transit1.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pytransit.data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pytransit.data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pytransit.data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pytransit.data' to be distributed and are already explicitly excluding 'pytransit.data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pytransit.data.CGI' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pytransit.data.CGI' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pytransit.data.CGI' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pytransit.data.CGI' to be distributed and are already explicitly excluding 'pytransit.data.CGI' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pytransit.genomes' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pytransit.genomes' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pytransit.genomes' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pytransit.genomes' to be distributed and are already explicitly excluding 'pytransit.genomes' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying src/pytransit/DejaVuSans.ttf -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit creating /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/COG_roles.dat -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/GO_associated_Rvs-3-11-18.txt -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/GO_associated_Rvs.csv -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/GO_term_names.dat -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/GO_terms_for_each_Rv.obo-3-11-18.txt -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/H37Rv.sanger_associated_RVS.csv -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/H37Rv_COG_roles.dat -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/H37Rv_GO_terms.txt -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/H37Rv_sanger_roles.dat -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/README.md -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/cholesterol_H37Rv_merged.wig -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/cholesterol_H37Rv_rep1.wig -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/cholesterol_H37Rv_rep2.wig -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/cholesterol_H37Rv_rep3.wig -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/cholesterol_glycerol_combined.dat -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/glycerol_H37Rv_merged.wig -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/glycerol_H37Rv_rep1.wig -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/glycerol_H37Rv_rep2.wig -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/iron_combined_wig4.txt -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/iron_samples_metadata.txt -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/samples_metadata_cg.txt -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/samples_metadata_cg_covar.txt -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/samples_metadata_cg_interactions.txt -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/sanger_roles.dat -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/smeg_COG_roles.dat -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data copying src/pytransit/data/smeg_GO_terms.txt -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data creating /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/CGI copying src/pytransit/data/CGI/IDs.H37Rv.CRISPRi.lib.txt -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/CGI copying src/pytransit/data/CGI/RIF_D1_combined_counts.txt -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/CGI copying src/pytransit/data/CGI/samples_metadata.txt -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/CGI copying src/pytransit/data/CGI/sgRNA_info.txt -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/CGI copying src/pytransit/data/CGI/uninduced_ATC_counts.txt -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/CGI creating /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes copying src/pytransit/genomes/BCG.fna -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes copying src/pytransit/genomes/BCG.prot_table -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes copying src/pytransit/genomes/H37Rv.fna -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes copying src/pytransit/genomes/H37Rv.prot_table -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes copying src/pytransit/genomes/H37RvBD.fna -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes copying src/pytransit/genomes/H37RvBD.prot_table -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes copying src/pytransit/genomes/H37RvBD_mod3.prot_table -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes copying src/pytransit/genomes/H37RvMA2.fna -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes copying src/pytransit/genomes/H37RvMA2.prot_table -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes copying src/pytransit/genomes/genomes.html -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes copying src/pytransit/genomes/mc2_155_tamu.fna -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes copying src/pytransit/genomes/mc2_155_tamu.prot_table -> /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/tnseq-transit-3.3.12' dh_auto_test -- --system=custom --test-args="PYTHONPATH=tests {interpreter} -m unittest -v tests/*.py" I: pybuild base:311: PYTHONPATH=tests python3.13 -m unittest -v tests/*.py test_Binomial (tests.test_analysis_methods.TestMethods.test_Binomial) ... /build/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:913: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:913: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:930: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:930: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:1290: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:1217: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:521: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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] Running Binomial Method... 0.7% [binomial] Running Binomial Method... 0.8% [binomial] Running Binomial Method... 0.9% [binomial] Running Binomial Method... 1.0% [binomial] Running Binomial Method... 1.1% [binomial] Running Binomial Method... 1.2% [binomial] Running Binomial Method... 1.3% [binomial] Running Binomial Method... 1.4% [binomial] Running Binomial Method... 1.5% [binomial] Running Binomial Method... 1.5% [binomial] Running Binomial Method... 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Running Binomial Method... 36.9% [binomial] Running Binomial Method... 37.0% [binomial] Running Binomial Method... 37.1% [binomial] Running Binomial Method... 37.2% [binomial] Running Binomial Method... 37.3% [binomial] Running Binomial Method... 37.4% [binomial] Running Binomial Method... 37.5% [binomial] Running Binomial Method... 37.5% [binomial] Running Binomial Method... 37.6% [binomial] Running Binomial Method... 37.7% [binomial] Running Binomial Method... 37.8% [binomial] Running Binomial Method... 37.9% [binomial] 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% 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Method... 47.2% [binomial] Running Binomial Method... 47.3% [binomial] Running Binomial Method... 47.4% [binomial] Running Binomial Method... 47.5% [binomial] Running Binomial Method... 47.5% [binomial] Running Binomial Method... 47.6% [binomial] Running Binomial Method... 47.7% [binomial] Running Binomial Method... 47.8% [binomial] Running Binomial Method... 47.9% [binomial] Running Binomial Method... 48.0% [binomial] Running Binomial Method... 48.1% [binomial] Running Binomial Method... 48.2% [binomial] Running Binomial Method... 48.3% [binomial] Running Binomial Method... 48.4% [binomial] Running Binomial Method... 48.5% [binomial] Running Binomial Method... 48.5% [binomial] Running Binomial Method... 48.6% [binomial] Running Binomial Method... 48.7% [binomial] Running Binomial Method... 48.8% [binomial] Running Binomial Method... 48.9% [binomial] Running Binomial Method... 49.0% [binomial] Running Binomial Method... 49.1% [binomial] Running Binomial Method... 49.2% [binomial] 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Running Binomial Method... 55.5% [binomial] Running Binomial Method... 55.5% [binomial] Running Binomial Method... 55.6% [binomial] Running Binomial Method... 55.7% [binomial] Running Binomial Method... 55.8% [binomial] Running Binomial Method... 55.9% [binomial] Running Binomial Method... 56.0% [binomial] Running Binomial Method... 56.1% [binomial] Running Binomial Method... 56.2% [binomial] Running Binomial Method... 56.3% [binomial] Running Binomial Method... 56.4% [binomial] Running Binomial Method... 56.5% [binomial] Running Binomial Method... 56.5% [binomial] Running Binomial Method... 56.6% [binomial] Running Binomial Method... 56.7% [binomial] Running Binomial Method... 56.8% [binomial] Running Binomial Method... 56.9% [binomial] Running Binomial Method... 57.0% [binomial] Running Binomial Method... 57.1% [binomial] Running Binomial Method... 57.2% [binomial] Running Binomial Method... 57.3% [binomial] Running Binomial Method... 57.4% [binomial] Running Binomial Method... 57.5% 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Method... 65.7% [binomial] Running Binomial Method... 65.8% [binomial] Running Binomial Method... 65.9% [binomial] Running Binomial Method... 66.0% [binomial] Running Binomial Method... 66.1% [binomial] Running Binomial Method... 66.2% [binomial] Running Binomial Method... 66.3% [binomial] Running Binomial Method... 66.4% [binomial] Running Binomial Method... 66.5% [binomial] Running Binomial Method... 66.5% [binomial] Running Binomial Method... 66.6% [binomial] Running Binomial Method... 66.7% [binomial] Running Binomial Method... 66.8% [binomial] Running Binomial Method... 66.9% [binomial] Running Binomial Method... 67.0% [binomial] Running Binomial Method... 67.1% [binomial] Running Binomial Method... 67.2% [binomial] Running Binomial Method... 67.3% [binomial] Running Binomial Method... 67.4% [binomial] Running Binomial Method... 67.5% [binomial] Running Binomial Method... 67.5% [binomial] Running Binomial Method... 67.6% [binomial] Running Binomial Method... 67.7% [binomial] Running Binomial Method... 67.8% [binomial] Running Binomial Method... 67.9% [binomial] Running Binomial Method... 68.0% [binomial] Running Binomial Method... 68.1% [binomial] Running Binomial Method... 68.2% [binomial] Running Binomial Method... 68.3% [binomial] Running Binomial Method... 68.4% [binomial] Running Binomial Method... 68.5% [binomial] Running Binomial Method... 68.5% [binomial] Running Binomial Method... 68.6% [binomial] Running Binomial Method... 68.7% [binomial] Running Binomial Method... 68.8% [binomial] 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% [binomial] Running Binomial Method... 71.0% [binomial] Running Binomial Method... 71.1% [binomial] Running Binomial Method... 71.2% [binomial] Running Binomial Method... 71.3% [binomial] Running Binomial Method... 71.4% [binomial] Running Binomial Method... 71.5% [binomial] Running Binomial Method... 71.5% [binomial] Running Binomial Method... 71.6% [binomial] Running Binomial Method... 71.7% [binomial] Running Binomial Method... 71.8% [binomial] Running Binomial 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Running Binomial Method... 74.0% [binomial] Running Binomial Method... 74.1% [binomial] Running Binomial Method... 74.2% [binomial] Running Binomial Method... 74.3% [binomial] Running Binomial Method... 74.4% [binomial] Running Binomial Method... 74.5% [binomial] Running Binomial Method... 74.5% [binomial] Running Binomial Method... 74.6% [binomial] Running Binomial Method... 74.7% [binomial] Running Binomial Method... 74.8% [binomial] Running Binomial Method... 74.9% [binomial] Running Binomial Method... 75.0% [binomial] 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% 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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% 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Running Binomial Method... 86.4% [binomial] Running Binomial Method... 86.5% [binomial] Running Binomial Method... 86.5% [binomial] Running Binomial Method... 86.6% [binomial] Running Binomial Method... 86.7% [binomial] Running Binomial Method... 86.8% [binomial] Running Binomial Method... 86.9% [binomial] Running Binomial Method... 87.0% [binomial] Running Binomial Method... 87.1% [binomial] Running Binomial Method... 87.2% [binomial] Running Binomial Method... 87.3% [binomial] Running Binomial Method... 87.4% [binomial] Running Binomial Method... 87.5% [binomial] Running Binomial Method... 87.5% [binomial] Running Binomial Method... 87.6% [binomial] Running Binomial Method... 87.7% [binomial] Running Binomial Method... 87.8% [binomial] Running Binomial Method... 87.9% [binomial] Running Binomial Method... 88.0% [binomial] Running Binomial Method... 88.1% [binomial] Running Binomial Method... 88.2% [binomial] Running Binomial Method... 88.3% [binomial] Running Binomial Method... 88.4% 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Method... 96.6% [binomial] Running Binomial Method... 96.7% [binomial] Running Binomial Method... 96.8% [binomial] Running Binomial Method... 96.9% [binomial] Running Binomial Method... 97.0% [binomial] Running Binomial Method... 97.1% [binomial] Running Binomial Method... 97.2% [binomial] Running Binomial Method... 97.3% [binomial] Running Binomial Method... 97.4% [binomial] Running Binomial Method... 97.5% [binomial] Running Binomial Method... 97.5% [binomial] Running Binomial Method... 97.6% [binomial] Running Binomial Method... 97.7% [binomial] Running Binomial Method... 97.8% [binomial] Running Binomial Method... 97.9% [binomial] Running Binomial Method... 98.0% [binomial] Running Binomial Method... 98.1% [binomial] Running Binomial Method... 98.2% [binomial] Running Binomial Method... 98.3% [binomial] Running Binomial Method... 98.4% [binomial] Running Binomial Method... 98.5% [binomial] Running Binomial Method... 98.5% [binomial] Running Binomial Method... 98.6% [binomial] Running Binomial Method... 98.7% [binomial] Running Binomial Method... 98.8% [binomial] Running Binomial Method... 98.9% [binomial] Running Binomial Method... 99.0% [binomial] Running Binomial Method... 99.1% [binomial] Running Binomial Method... 99.2% [binomial] Running Binomial Method... 99.3% [binomial] Running Binomial Method... 99.4% [binomial] Running Binomial Method... 99.5% [binomial] Running Binomial Method... 99.5% [binomial] Running Binomial Method... 99.6% [binomial] Running Binomial Method... 99.7% [binomial] 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.test_GI) ... /build/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:913: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:913: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:913: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:930: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:930: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:930: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/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] analyzing Rv0244c (0.0% done) [gi] Running GI Method... 4% [gi] analyzing Rv0362 (2.0% done) [gi] Running GI Method... 6% [gi] analyzing Rv0450c (4.0% done) [gi] Running GI Method... 8% [gi] analyzing Rv0485 (6.0% done) [gi] Running GI Method... 10% [gi] analyzing Rv0694 (8.0% done) [gi] Running GI Method... 12% [gi] analyzing Rv0761c (10.0% done) [gi] Running GI Method... 14% [gi] analyzing Rv1129c (12.0% done) [gi] Running GI Method... 16% [gi] analyzing Rv1130 (14.0% done) [gi] Running GI Method... 18% [gi] analyzing Rv1183 (16.0% done) [gi] Running GI Method... 20% [gi] analyzing Rv1428c (18.0% done) [gi] Running GI Method... 22% [gi] analyzing Rv3200c (20.0% done) [gi] Running GI Method... 24% [gi] analyzing Rv3559c (22.0% done) [gi] Running GI Method... 25% [gi] analyzing Rv3564 (24.0% done) [gi] Running GI Method... 27% [gi] analyzing Rv3575c (26.0% done) [gi] Running GI Method... 29% [gi] analyzing Rv0381c (28.0% done) [gi] Running GI Method... 31% [gi] analyzing Rv1432 (30.0% done) [gi] Running GI Method... 33% [gi] analyzing Rv3543c (32.0% done) [gi] Running GI Method... 35% [gi] analyzing Rv3570c (34.0% done) [gi] Running GI Method... 37% [gi] analyzing Rv0495c (36.0% done) [gi] Running GI Method... 39% [gi] analyzing Rv0805 (38.0% done) [gi] Running GI Method... 41% [gi] analyzing Rvnr01 (40.0% done) [gi] Running GI Method... 43% [gi] analyzing Rv3924c (42.0% done) [gi] Running GI Method... 45% [gi] analyzing Rv3923c (44.0% done) [gi] Running GI Method... 47% [gi] analyzing Rv3922c (46.0% done) [gi] Running GI Method... 49% [gi] analyzing Rv3921c (48.0% done) [gi] Running GI Method... 51% [gi] analyzing Rv3920c (50.0% done) [gi] Running GI Method... 53% [gi] analyzing Rv3918c (52.0% done) [gi] Running GI Method... 55% [gi] analyzing Rv3917c (54.0% done) [gi] Running GI Method... 57% [gi] analyzing Rv3916c (56.0% done) [gi] Running GI Method... 59% [gi] analyzing Rv3915 (58.0% done) [gi] Running GI Method... 61% [gi] analyzing Rv1132 (60.0% done) [gi] Running GI Method... 63% [gi] analyzing Rv0499 (62.0% done) [gi] Running GI Method... 65% [gi] analyzing Rv2190c (64.0% done) [gi] Running GI Method... 67% [gi] analyzing Rv2207 (66.0% done) [gi] Running GI Method... 69% [gi] analyzing Rv2347c (68.0% done) [gi] Running GI Method... 71% [gi] analyzing Rv2567 (70.0% done) [gi] Running GI Method... 73% [gi] analyzing Rv2887 (72.0% done) [gi] Running GI Method... 75% [gi] analyzing Rv3005c (74.0% done) [gi] Running GI Method... 76% [gi] analyzing Rv1111c (76.0% done) [gi] Running GI Method... 78% [gi] analyzing Rv1072 (78.0% done) [gi] Running GI Method... 80% [gi] analyzing Rv2958c (80.0% done) [gi] Running GI Method... 82% [gi] analyzing Rv3552 (82.0% done) [gi] Running GI Method... 84% [gi] analyzing Rv0129c (84.0% done) [gi] Running GI Method... 86% [gi] analyzing Rv1821 (86.0% done) [gi] Running GI Method... 88% [gi] analyzing Rv2224c (88.0% done) [gi] Running GI Method... 90% [gi] analyzing Rv3567c (90.0% done) [gi] Running GI Method... 92% [gi] analyzing Rv0924c (92.0% done) [gi] Running GI Method... 94% [gi] analyzing Rv0249c (94.0% done) [gi] Running GI Method... 96% [gi] analyzing Rv2021c (96.0% done) [gi] Running GI Method... 98% [gi] analyzing Rv2694c (98.0% done) [gi] Running GI Method... 100% /usr/lib/python3.13/unittest/case.py:606: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/tests/testoutput.txt' mode='w' encoding='UTF-8'> if method() is not None: ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_Griffin (tests.test_analysis_methods.TestMethods.test_Griffin) ... [gi] analyzing Rv3586 (100.0% done) [gi] Adding File: /build/reproducible-path/tnseq-transit-3.3.12/tests/testoutput.txt [gi] Finished Genetic Interactions Method Removing output file... #################### tests.test_analysis_methods.TestMethods.test_Griffin #################### [griffin] Starting Griffin Method [griffin] Getting Data [griffin] Running Griffin Method... 2.0% [griffin] Running Griffin Method... 3.9% [griffin] Running Griffin Method... 5.9% [griffin] Running Griffin Method... 7.8% [griffin] Running Griffin Method... 9.8% [griffin] Running Griffin Method... 11.8% [griffin] Running Griffin Method... 13.7% [griffin] Running Griffin Method... 15.7% [griffin] Running Griffin Method... 17.6% [griffin] Running Griffin Method... 19.6% [griffin] Running Griffin Method... 21.6% [griffin] Running Griffin Method... 23.5% [griffin] Running Griffin Method... 25.5% [griffin] Running Griffin Method... 27.5% [griffin] Running Griffin Method... 29.4% [griffin] Running Griffin Method... 31.4% [griffin] Running Griffin Method... 33.3% [griffin] Running Griffin Method... 35.3% [griffin] Running Griffin Method... 37.3% [griffin] Running Griffin Method... 39.2% [griffin] Running Griffin Method... 41.2% [griffin] Running Griffin Method... 43.1% [griffin] Running Griffin Method... 45.1% [griffin] Running Griffin Method... 47.1% [griffin] Running Griffin Method... 49.0% [griffin] Running Griffin Method... 51.0% [griffin] Running Griffin Method... 52.9% [griffin] Running Griffin Method... 54.9% [griffin] Running Griffin Method... 56.9% [griffin] Running Griffin Method... 58.8% [griffin] Running Griffin Method... 60.8% [griffin] Running Griffin Method... 62.7% [griffin] Running Griffin Method... 64.7% [griffin] Running Griffin Method... 66.7% [griffin] Running Griffin Method... 68.6% [griffin] Running Griffin Method... 70.6% [griffin] Running Griffin Method... 72.5% [griffin] Running Griffin Method... 74.5% [griffin] Running Griffin Method... 76.5% [griffin] Running Griffin Method... 78.4% [griffin] Running Griffin Method... 80.4% [griffin] Running Griffin Method... 82.4% [griffin] Running Griffin Method... 84.3% [griffin] Running Griffin Method... 86.3% [griffin] Running Griffin Method... 88.2% [griffin] Running Griffin Method... 90.2% [griffin] Running Griffin Method... 92.2% [griffin] Running Griffin Method... 94.1% [griffin] Running Griffin Method... 96.1% [griffin] Running Griffin Method... 98.0% [griffin] Running Griffin Method... 100.0% ok test_Gumbel (tests.test_analysis_methods.TestMethods.test_Gumbel) ... [griffin] [griffin] Adding File: /build/reproducible-path/tnseq-transit-3.3.12/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 with Binomial Essentiality Calls... 0.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 0.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 0.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 0.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 0.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 0.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 0.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 0.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 0.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 1.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 1.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 1.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 1.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 1.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 1.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 1.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 1.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 1.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 1.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 1.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 2.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 2.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 2.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 2.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 2.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 2.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 2.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 2.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 2.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 2.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 2.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 3.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 3.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 3.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 3.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 3.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 3.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 3.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 3.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 3.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 3.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 3.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 4.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 4.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 4.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 4.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 4.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 4.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 4.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 4.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 4.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 4.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 4.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 5.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 5.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 5.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 5.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 5.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 5.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 5.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 5.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 5.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 5.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 5.9% [gumbel] Running 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[gumbel] Running Gumbel Method with Binomial Essentiality Calls... 8.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 8.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 8.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 8.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 8.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 9.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 9.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 9.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 9.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 9.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 9.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 9.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 9.6% [gumbel] Running Gumbel Method with Binomial Essentiality 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Binomial Essentiality Calls... 11.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 11.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 11.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 11.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 11.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 11.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 11.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 11.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 11.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 11.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 11.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 12.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 12.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 12.2% [gumbel] 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Binomial Essentiality Calls... 25.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 26.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 26.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 26.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 26.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 26.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 26.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 26.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 26.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 26.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 26.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 26.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 27.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 27.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 27.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 27.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 27.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 27.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 27.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 27.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 27.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 27.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 27.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 28.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 28.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 28.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 28.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 28.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 28.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 28.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 28.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 28.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 28.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 28.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 29.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 29.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 29.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 29.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 29.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 29.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 29.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 29.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 29.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 29.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 29.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 30.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 30.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 30.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 30.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 30.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 30.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 30.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 30.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 30.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 30.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 30.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 31.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 31.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 31.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 31.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 31.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 31.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 31.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 31.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 31.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 31.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 31.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 32.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 32.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 32.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 32.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 32.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 32.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 32.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 32.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 32.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 32.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 32.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 33.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 33.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 33.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 33.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 33.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 33.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 33.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 33.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 33.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 33.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 33.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 34.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 34.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 34.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 34.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 34.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 34.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 34.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 34.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 34.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 34.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 34.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 35.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 35.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 35.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 35.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 35.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 35.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 35.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 35.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 35.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 35.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 35.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 36.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 36.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 36.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 36.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 36.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 36.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 36.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 36.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 36.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 36.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 36.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 37.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 37.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 37.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 37.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 37.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 37.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 37.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 37.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 37.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 37.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 37.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 38.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 38.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 38.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 38.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 38.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 38.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 38.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 38.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 38.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 38.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 38.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 39.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 39.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 39.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 39.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 39.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 39.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 39.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 39.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 39.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 39.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 39.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 40.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 40.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 40.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 40.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 40.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 40.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 40.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 40.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 40.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 40.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 40.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 41.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 41.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 41.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 41.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 41.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 41.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 41.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 41.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 41.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 41.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 41.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 42.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 42.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 42.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 42.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 42.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 42.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 42.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 42.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 42.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 42.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 42.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 43.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 43.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 43.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 43.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 43.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 43.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 43.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 43.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 43.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 43.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 43.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 44.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 44.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 44.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 44.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 44.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 44.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 44.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 44.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 44.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 44.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 44.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 45.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 45.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 45.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 45.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 45.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 45.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 45.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 45.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 45.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 45.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 45.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 46.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 46.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 46.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 46.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 46.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 46.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 46.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 46.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 46.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 46.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 46.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 47.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 47.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 47.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 47.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 47.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 47.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 47.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 47.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 47.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 47.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 47.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 48.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 48.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 48.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 48.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 48.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 48.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 48.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 48.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 48.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 48.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 48.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 49.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 49.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 49.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 49.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 49.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 49.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 49.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 49.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 49.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 49.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 49.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 50.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 50.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 50.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 50.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 50.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 50.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 50.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 50.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 50.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 50.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 50.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 51.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 51.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 51.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 51.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 51.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 51.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 51.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 51.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 51.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 51.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 51.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 52.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 52.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 52.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 52.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 52.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 52.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 52.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 52.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 52.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 52.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 52.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 53.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 53.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 53.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 53.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 53.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 53.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 53.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 53.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 53.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 53.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 53.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 54.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 54.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 54.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 54.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 54.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 54.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 54.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 54.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 54.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 54.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 54.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 55.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 55.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 55.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 55.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 55.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 55.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 55.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 55.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 55.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 55.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 55.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 56.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 56.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 56.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 56.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 56.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 56.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 56.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 56.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 56.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 56.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 56.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 57.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 57.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 57.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 57.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 57.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 57.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 57.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 57.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 57.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 57.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 57.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 58.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 58.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 58.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 58.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 58.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 58.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 58.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 58.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 58.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 58.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 58.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 59.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 59.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 59.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 59.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 59.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 59.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 59.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 59.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 59.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 59.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 59.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 60.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 60.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 60.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 60.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 60.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 60.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 60.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 60.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 60.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 60.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 60.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 61.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 61.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 61.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 61.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 61.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 61.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 61.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 61.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 61.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 61.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 61.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 62.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 62.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 62.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 62.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 62.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 62.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 62.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 62.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 62.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 62.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 62.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 63.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 63.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 63.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 63.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 63.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 63.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 63.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 63.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 63.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 63.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 63.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 64.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 64.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 64.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 64.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 64.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 64.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 64.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 64.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 64.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 64.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 64.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 65.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 65.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 65.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 65.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 65.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 65.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 65.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 65.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 65.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 65.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 65.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 66.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 66.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 66.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 66.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 66.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 66.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 66.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 66.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 66.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 66.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 66.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 67.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 67.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 67.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 67.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 67.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 67.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 67.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 67.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 67.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 67.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 67.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 68.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 68.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 68.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 68.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 68.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 68.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 68.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 68.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 68.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 68.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 68.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 69.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 69.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 69.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 69.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 69.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 69.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 69.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 69.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 69.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 69.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 69.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 70.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 70.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 70.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 70.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 70.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 70.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 70.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 70.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 70.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 70.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 70.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 71.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 71.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 71.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 71.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 71.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 71.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 71.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 71.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 71.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 71.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 71.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 72.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 72.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 72.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 72.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 72.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 72.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 72.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 72.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 72.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 72.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 72.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 73.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 73.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 73.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 73.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 73.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 73.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 73.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 73.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 73.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 73.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 73.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 74.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 74.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 74.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 74.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 74.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 74.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 74.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 74.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 74.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 74.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 74.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 75.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 75.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 75.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 75.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 75.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 75.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 75.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 75.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 75.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 75.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 75.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 76.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 76.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 76.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 76.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 76.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 76.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 76.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 76.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 76.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 76.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 76.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 77.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 77.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 77.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 77.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 77.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 77.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 77.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 77.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 77.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 77.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 77.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 78.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 78.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 78.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 78.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 78.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 78.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 78.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 78.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 78.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 78.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 78.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 79.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 79.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 79.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 79.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 79.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 79.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 79.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 79.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 79.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 79.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 79.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 80.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 80.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 80.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 80.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 80.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 80.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 80.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 80.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 80.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 80.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 80.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 81.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 81.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 81.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 81.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 81.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 81.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 81.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 81.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 81.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 81.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 81.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 82.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 82.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 82.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 82.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 82.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 82.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 82.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 82.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 82.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 82.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 82.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 83.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 83.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 83.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 83.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 83.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 83.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 83.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 83.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 83.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 83.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 83.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 84.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 84.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 84.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 84.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 84.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 84.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 84.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 84.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 84.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 84.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 84.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 85.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 85.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 85.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 85.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 85.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 85.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 85.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 85.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 85.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 85.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 85.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 86.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 86.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 86.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 86.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 86.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 86.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 86.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 86.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 86.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 86.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 86.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 87.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 87.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 87.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 87.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 87.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 87.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 87.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 87.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 87.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 87.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 87.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 88.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 88.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 88.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 88.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 88.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 88.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 88.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 88.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 88.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 88.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 88.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 89.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 89.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 89.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 89.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 89.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 89.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 89.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 89.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 89.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 89.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 89.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 90.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 90.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 90.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 90.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 90.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 90.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 90.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 90.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 90.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 90.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 90.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 91.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 91.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 91.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 91.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 91.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 91.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 91.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 91.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 91.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 91.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 91.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 92.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 92.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 92.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 92.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 92.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 92.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 92.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 92.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 92.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 92.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 92.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 93.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 93.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 93.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 93.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 93.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 93.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 93.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 93.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 93.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 93.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 93.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 94.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 94.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 94.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 94.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 94.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 94.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 94.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 94.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 94.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 94.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 94.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 95.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 95.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 95.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 95.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 95.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 95.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 95.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 95.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 95.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 95.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 95.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 96.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 96.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 96.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 96.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 96.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 96.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 96.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 96.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 96.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 96.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 96.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 97.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 97.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 97.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 97.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 97.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 97.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 97.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 97.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 97.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 97.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 97.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 98.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 98.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 98.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 98.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 98.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 98.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 98.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 98.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 98.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 98.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 98.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 99.0% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 99.1% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 99.2% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 99.3% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 99.4% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 99.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 99.5% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 99.6% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 99.7% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 99.8% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 99.9% [gumbel] Running Gumbel Method with Binomial Essentiality Calls... 100.0% ok test_HMM (tests.test_analysis_methods.TestMethods.test_HMM) ... /build/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/analysis/hmm.py:194: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:913: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/tests/data/test.wig' mode='r' encoding='UTF-8'> for line in open(path): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:930: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/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.test_anova) ... /build/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:84: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/data/samples_metadata_cg.txt' mode='r' encoding='UTF-8'> for line in open(metadata_file): ResourceWarning: Enable tracemalloc to get the object allocation traceback /build/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:124: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/testoutput.txt.sites.txt [hmm] Creating HMM Genes Level Output [hmm] Adding File: /build/reproducible-path/tnseq-transit-3.3.12/tests/testoutput.txt.genes.txt [hmm] Finished HMM Method #################### 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/reproducible-path/tnseq-transit-3.3.12/tests/transit_test.py:89: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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.test_resampling) ... /build/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:913: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:913: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:930: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:930: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:913: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:913: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:913: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:930: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:930: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:930: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:1290: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:1217: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:521: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/testoutput.txt [anova] Finished Anova analysis [anova] Time: 0.3s Removing output file... #################### tests.test_analysis_methods.TestMethods.test_resampling #################### [resampling] site_restricted=False [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/reproducible-path/tnseq-transit-3.3.12/tests/transit_test.py:89: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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.test_resampling_adaptive) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 35 [resampling] Time: 8.48s [resampling] Finished resampling Method Removing output file... #################### tests.test_analysis_methods.TestMethods.test_resampling_adaptive #################### [resampling] site_restricted=False [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.test_resampling_combined_wig) ... /build/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:84: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/data/samples_metadata_cg.txt' mode='r' encoding='UTF-8'> for line in open(metadata_file): ResourceWarning: Enable tracemalloc to get the object allocation traceback [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 35 [resampling] Time: 5.49s [resampling] Finished resampling Method Removing output file... #################### tests.test_analysis_methods.TestMethods.test_resampling_combined_wig #################### [resampling] site_restricted=False [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.test_resampling_histogram) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 35 [resampling] Time: 4.27s [resampling] Finished resampling Method 37 35 Removing output file... #################### tests.test_analysis_methods.TestMethods.test_resampling_histogram #################### [resampling] site_restricted=False [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.test_resampling_multistrain) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 34 [resampling] Time: 10.53s [resampling] Finished resampling Method Removing histogram files Removing output file... #################### tests.test_analysis_methods.TestMethods.test_resampling_multistrain #################### [resampling] site_restricted=False [resampling] Starting resampling Method [resampling] Getting Data [resampling] Multiple annotation files found [resampling] Mapping ctrl data to /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test.prot_table, exp data to /build/reproducible-path/tnseq-transit-3.3.12/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.test_utest) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 35 [resampling] Time: 18.45s [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.test_zinb) ... skipped 'requires R, rpy2' test_zinb_covariates (tests.test_analysis_methods.TestMethods.test_zinb_covariates) ... skipped 'requires R, rpy2' test_zinb_interactions (tests.test_analysis_methods.TestMethods.test_zinb_interactions) ... skipped 'requires R, rpy2' test_TTR (tests.test_norm_methods.TestNormMethods.test_TTR) ... ok test_nonorm (tests.test_norm_methods.TestNormMethods.test_nonorm) ... ok test_resampling_NZMean (tests.test_norm_methods.TestNormMethods.test_resampling_NZMean) ... [utest] [utest] Performing Benjamini-Hochberg Correction [utest] Adding File: /build/reproducible-path/tnseq-transit-3.3.12/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] site_restricted=False [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.test_resampling_Quantile) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 [resampling] Time: 1.14s [resampling] Finished resampling Method Removing output file... #################### tests.test_norm_methods.TestNormMethods.test_resampling_Quantile #################### [resampling] site_restricted=False [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/reproducible-path/tnseq-transit-3.3.12/tests/transit_test.py:75: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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.test_resampling_TTR) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 [resampling] Time: 1.29s [resampling] Finished resampling Method Removing output file... #################### tests.test_norm_methods.TestNormMethods.test_resampling_TTR #################### [resampling] site_restricted=False [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.test_resampling_TotReads) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 [resampling] Time: 1.08s [resampling] Finished resampling Method Removing output file... #################### tests.test_norm_methods.TestNormMethods.test_resampling_TotReads #################### [resampling] site_restricted=False [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.test_resampling_ZINFNB) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 [resampling] Time: 0.99s [resampling] Finished resampling Method Removing output file... #################### tests.test_norm_methods.TestNormMethods.test_resampling_ZINFNB #################### [resampling] site_restricted=False [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.test_resampling_nonorm) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 [resampling] Time: 3.28s [resampling] Finished resampling Method Removing output file... #################### tests.test_norm_methods.TestNormMethods.test_resampling_nonorm #################### [resampling] site_restricted=False [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.test_cleanargs_flag_arguments_w_quotes) ... ok test_cleanargs_flag_arguments_with_double_dash (tests.test_pytransit_tools.TestTnSeqTools.test_cleanargs_flag_arguments_with_double_dash) ... ok test_cleanargs_flag_without_arguments (tests.test_pytransit_tools.TestTnSeqTools.test_cleanargs_flag_without_arguments) ... ok test_cleanargs_negative_arguments (tests.test_pytransit_tools.TestTnSeqTools.test_cleanargs_negative_arguments) ... ok test_cleanargs_positional_arguments (tests.test_pytransit_tools.TestTnSeqTools.test_cleanargs_positional_arguments) ... ok test_cleanargs_positional_arguments_w_quotes (tests.test_pytransit_tools.TestTnSeqTools.test_cleanargs_positional_arguments_w_quotes) ... ok test_file_types (tests.test_pytransit_tools.TestTnSeqTools.test_file_types) ... ok test_genes_creation_fromdata (tests.test_pytransit_tools.TestTnSeqTools.test_genes_creation_fromdata) ... /build/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:1290: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:1217: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytransit/tnseq_tools.py:521: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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.test_genes_creation_fromwig) ... ok test_normalization (tests.test_pytransit_tools.TestTnSeqTools.test_normalization) ... ok test_read_data (tests.test_pytransit_tools.TestTnSeqTools.test_read_data) ... ok test_tpp_flag_primer (tests.test_tpp.TestTPP.test_tpp_flag_primer) ... skipped 'requires local data file' test_tpp_multicontig_auto_replicon_ids (tests.test_tpp.TestTPP.test_tpp_multicontig_auto_replicon_ids) ... [tn_preprocess] running pre-processing on /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig-1.fastq and [tn_preprocess] protocol: Sassetti [tn_preprocess] transposon type: Himar1 [tn_preprocess] One reference genome specified: /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna, containing 3 records. [tn_preprocess] Autogenerating replicon_ids... [tn_preprocess] extracting reads... [tn_preprocess] fastq2reads: /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig-1.fastq -> /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp.reads1 /build/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytpp/tpp_tools.py:85: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp.trimmed1 [tn_preprocess] prefix sequence: [tn_preprocess] Looking for start of Tn prefix within positions [0,20] /build/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytpp/tpp_tools.py:284: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna b'[bwa_index] Pack FASTA... 0.08 sec' b'[bwa_index] Construct BWT for the packed sequence...' b'[bwa_index] 1.80 seconds elapse.' b'[bwa_index] Update BWT... 0.02 sec' b'[bwa_index] Pack forward-only FASTA... 0.02 sec' b'[bwa_index] Construct SA from BWT and Occ... 1.11 sec' b'[main] Version: 0.7.18-r1243-dirty' b'[main] CMD: /usr/bin/bwa index /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna' b'[main] Real time: 3.034 sec; CPU: 3.035 sec' b'' [tn_preprocess] /usr/bin/bwa mem /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp.trimmed1 > /build/reproducible-path/tnseq-transit-3.3.12/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 0.241 CPU sec, 0.241 real sec' b'[main] Version: 0.7.18-r1243-dirty' b'[main] CMD: /usr/bin/bwa mem /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp.trimmed1' b'[main] Real time: 0.252 sec; CPU: 0.253 sec' b'' [tn_preprocess] tabulating template counts and statistics for reference genome /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytpp/tpp_tools.py:385: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytpp/tpp_tools.py:567: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp_1.wig [tn_preprocess] writing /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp_2.wig [tn_preprocess] writing /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp_3.wig /build/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytpp/tpp_tools.py:1116: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytpp/tpp_tools.py:1117: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/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 /build/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytpp/tpp_tools.py:1195: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp.trimmed1' mode='r' encoding='UTF-8'> for line in open(vars.trimmed1): ResourceWarning: Enable tracemalloc to get the object allocation traceback [tn_preprocess] writing /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp.tn_stats [tn_preprocess] Done. ok test_tpp_multicontig_empty_prefix (tests.test_tpp.TestTPP.test_tpp_multicontig_empty_prefix) ... [tn_preprocess] running pre-processing on /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig-1.fastq and [tn_preprocess] protocol: Sassetti [tn_preprocess] transposon type: Himar1 [tn_preprocess] One reference genome specified: /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna, containing 3 records. [tn_preprocess] extracting reads... [tn_preprocess] fastq2reads: /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig-1.fastq -> /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp.reads1 [tn_preprocess] assuming single-ended reads [tn_preprocess] creating /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp.trimmed1 [tn_preprocess] prefix sequence: [tn_preprocess] Looking for start of Tn prefix within positions [0,20] [tn_preprocess] mapping reads using BWA...(this takes a couple of minutes) [tn_preprocess] /usr/bin/bwa mem /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp.trimmed1 > /build/reproducible-path/tnseq-transit-3.3.12/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 0.232 CPU sec, 0.231 real sec' b'[main] Version: 0.7.18-r1243-dirty' b'[main] CMD: /usr/bin/bwa mem /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp.trimmed1' b'[main] Real time: 0.244 sec; CPU: 0.245 sec' b'' [tn_preprocess] tabulating template counts and statistics for reference genome /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna [tn_preprocess] writing /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp_a.wig [tn_preprocess] writing /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp_b.wig [tn_preprocess] writing /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp_c.wig [tn_preprocess] writing /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp.tn_stats [tn_preprocess] Done. ok test_tpp_noflag_primer (tests.test_tpp.TestTPP.test_tpp_noflag_primer) ... skipped 'requires local data file' test_tpp_protocol_mme1 (tests.test_tpp.TestTPP.test_tpp_protocol_mme1) ... skipped 'requires local data file' ---------------------------------------------------------------------- Ran 39 tests in 89.891s OK (skipped=6) [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 [resampling] Time: 0.99s [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 #################### /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig-1.fastq # title: Tn-Seq Pre-Processor # date: 02/05/2025 22:31:58 # command: python python3.13 -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/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig-1.fastq # read2: # ref_genome: /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna # replicon_ids: 1,2,3 # total_reads (or read pairs): 2500 # truncated_reads 156 (genomic inserts shorter than the read length; ADAP2 appears in read1) # 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 # Break-down of total reads (2500): # -12 reads (-0.5%) lack the expected Tn prefix # Break-down of trimmed reads with valid Tn prefix (2500): # primer_matches: 36 reads (1.4%) contain CTAGAGGGCCCAATTCGCCCTATAGTGAGT (Himar1) # vector_matches: 36 reads (1.4%) contain CTAGACCGTCCAGTCTGGCAGGCCGGAAAC (phiMycoMarT7) # adapter_matches: 14 reads (0.6%) 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 #################### /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig-1.fastq # title: Tn-Seq Pre-Processor # date: 02/05/2025 22:32:00 # command: python python3.13 -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/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig-1.fastq # read2: # ref_genome: /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna # replicon_ids: a,b,c # total_reads (or read pairs): 2500 # truncated_reads 156 (genomic inserts shorter than the read length; ADAP2 appears in read1) # 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 # Break-down of total reads (2500): # -12 reads (-0.5%) lack the expected Tn prefix # Break-down of trimmed reads with valid Tn prefix (2500): # primer_matches: 36 reads (1.4%) contain CTAGAGGGCCCAATTCGCCCTATAGTGAGT (Himar1) # vector_matches: 36 reads (1.4%) contain CTAGACCGTCCAGTCTGGCAGGCCGGAAAC (phiMycoMarT7) # adapter_matches: 14 reads (0.6%) 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/reproducible-path/tnseq-transit-3.3.12' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/tnseq-transit/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing transit1.egg-info/PKG-INFO writing dependency_links to transit1.egg-info/dependency_links.txt writing entry points to transit1.egg-info/entry_points.txt writing requirements to transit1.egg-info/requires.txt writing top-level names to transit1.egg-info/top_level.txt reading manifest file 'transit1.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' adding license file 'LICENSE.md' writing manifest file 'transit1.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pytransit.data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pytransit.data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pytransit.data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pytransit.data' to be distributed and are already explicitly excluding 'pytransit.data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pytransit.data.CGI' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pytransit.data.CGI' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pytransit.data.CGI' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pytransit.data.CGI' to be distributed and are already explicitly excluding 'pytransit.data.CGI' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pytransit.genomes' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pytransit.genomes' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pytransit.genomes' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pytransit.genomes' to be distributed and are already explicitly excluding 'pytransit.genomes' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) running install_lib creating /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages creating /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytpp copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytpp/__init__.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytpp copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytpp/__main__.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytpp copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytpp/tpp_gui.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytpp copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytpp/tpp_tools.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytpp creating /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit creating /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/genomes copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes/mc2_155_tamu.prot_table -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/genomes copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes/mc2_155_tamu.fna -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/genomes copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes/genomes.html -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/genomes copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes/H37RvMA2.prot_table -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/genomes copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes/H37RvMA2.fna -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/genomes copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes/H37RvBD_mod3.prot_table -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/genomes copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes/H37RvBD.prot_table -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/genomes copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes/H37RvBD.fna -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/genomes copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes/H37Rv.prot_table -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/genomes copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes/H37Rv.fna -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/genomes copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes/BCG.prot_table -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/genomes copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/genomes/BCG.fna -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/genomes creating /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data creating /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data/CGI copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/CGI/uninduced_ATC_counts.txt -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data/CGI copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/CGI/sgRNA_info.txt -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data/CGI copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/CGI/samples_metadata.txt -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data/CGI copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/CGI/RIF_D1_combined_counts.txt -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data/CGI copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/CGI/IDs.H37Rv.CRISPRi.lib.txt -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data/CGI copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/smeg_GO_terms.txt -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/smeg_COG_roles.dat -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/sanger_roles.dat -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/samples_metadata_cg_interactions.txt -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/samples_metadata_cg_covar.txt -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/samples_metadata_cg.txt -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/iron_samples_metadata.txt -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/iron_combined_wig4.txt -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/glycerol_H37Rv_rep2.wig -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/glycerol_H37Rv_rep1.wig -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/glycerol_H37Rv_merged.wig -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/cholesterol_glycerol_combined.dat -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/cholesterol_H37Rv_rep3.wig -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/cholesterol_H37Rv_rep2.wig -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/cholesterol_H37Rv_rep1.wig -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/cholesterol_H37Rv_merged.wig -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/README.md -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/H37Rv_sanger_roles.dat -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/H37Rv_GO_terms.txt -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/H37Rv_COG_roles.dat -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/H37Rv.sanger_associated_RVS.csv -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/GO_terms_for_each_Rv.obo-3-11-18.txt -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/GO_term_names.dat -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/GO_associated_Rvs.csv -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/GO_associated_Rvs-3-11-18.txt -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/data/COG_roles.dat -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/data copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/DejaVuSans.ttf -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit creating /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/convert copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/convert/__init__.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/convert copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/convert/base.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/convert copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/convert/gff_to_prot_table.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/convert creating /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/export copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/export/__init__.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/export copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/export/base.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/export copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/export/combined_wig.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/export copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/export/igv.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/export copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/export/mean_counts.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/export copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/export/prot_table.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/export creating /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/CGI.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/__init__.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/anova.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/base.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/binomial.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/corrplot.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/example.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/gi.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/griffin.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/gumbel.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/heatmap.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/hmm.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/norm.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/normalize.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/pathway_enrichment.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/rankproduct.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/resampling.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/tn5gaps.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/tnseq_stats.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/ttnfitness.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/utest.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/analysis/zinb.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/__init__.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/__main__.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/draw_trash.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/fileDisplay.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/images.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/norm_tools.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/qcDisplay.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/stat_tools.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/tnseq_tools.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/transit_gui.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/transit_tools.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/trash.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/view_trash.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit creating /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/generic_tools copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/generic_tools/__init__.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/generic_tools copying /build/reproducible-path/tnseq-transit-3.3.12/.pybuild/cpython3_3.13/build/pytransit/generic_tools/file_system_py.py -> /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/generic_tools byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytpp/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytpp/__main__.py to __main__.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytpp/tpp_gui.py to tpp_gui.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytpp/tpp_tools.py to tpp_tools.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/convert/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/convert/base.py to base.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/convert/gff_to_prot_table.py to gff_to_prot_table.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/export/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/export/base.py to base.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/export/combined_wig.py to combined_wig.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/export/igv.py to igv.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/export/mean_counts.py to mean_counts.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/export/prot_table.py to prot_table.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/CGI.py to CGI.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/anova.py to anova.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/base.py to base.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/binomial.py to binomial.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/corrplot.py to corrplot.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/example.py to example.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/gi.py to gi.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/griffin.py to griffin.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/gumbel.py to gumbel.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/heatmap.py to heatmap.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/hmm.py to hmm.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/norm.py to norm.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/normalize.py to normalize.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/pathway_enrichment.py to pathway_enrichment.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/rankproduct.py to rankproduct.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/resampling.py to resampling.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/tn5gaps.py to tn5gaps.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/tnseq_stats.py to tnseq_stats.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/ttnfitness.py to ttnfitness.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/utest.py to utest.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/analysis/zinb.py to zinb.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/__main__.py to __main__.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/draw_trash.py to draw_trash.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/fileDisplay.py to fileDisplay.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/images.py to images.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/norm_tools.py to norm_tools.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/qcDisplay.py to qcDisplay.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/stat_tools.py to stat_tools.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/tnseq_tools.py to tnseq_tools.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/transit_gui.py to transit_gui.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/transit_tools.py to transit_tools.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/trash.py to trash.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/view_trash.py to view_trash.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/generic_tools/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/pytransit/generic_tools/file_system_py.py to file_system_py.cpython-313.pyc running install_egg_info Copying transit1.egg-info to /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/lib/python3.13/dist-packages/transit1-3.3.12.egg-info Skipping SOURCES.txt running install_scripts Installing tpp script to /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/bin Installing transit script to /build/reproducible-path/tnseq-transit-3.3.12/debian/tnseq-transit/usr/bin debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/tnseq-transit-3.3.12' mv debian/tnseq-transit/usr/bin/tpp debian/tnseq-transit/usr/bin/transit-tpp make[1]: Leaving directory '/build/reproducible-path/tnseq-transit-3.3.12' 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_3.3.12-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../tnseq-transit_3.3.12-1_arm64.buildinfo dpkg-genchanges --build=binary -O../tnseq-transit_3.3.12-1_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/1206982 and its subdirectories I: Current time: Wed Feb 5 22:32:40 -12 2025 I: pbuilder-time-stamp: 1738837960 Thu Feb 6 10:33:05 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Thu Feb 6 10:33:05 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Thu Feb 6 10:41:01 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Thu Feb 6 10:41:02 UTC 2025 I: tnseq-transit_3.3.12-1_arm64.changes: Format: 1.8 Date: Mon, 03 Feb 2025 15:06:19 +0100 Source: tnseq-transit Binary: tnseq-transit Architecture: arm64 Version: 3.3.12-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Alexandre Detiste Description: tnseq-transit - statistical calculations of essentiality of genes or genomic regi Closes: 1083799 Changes: tnseq-transit (3.3.12-1) unstable; urgency=medium . * Team Upload * New upstream version 3.3.12 * Patch-out generation of python3-pkg-resources dep (Closes: #1083799) . [ Andreas Tille ] * New upstream version 3.3.10 * Standards-Version: 4.7.0 (routine-update) * Refresh patches Checksums-Sha1: 5936225a7d2d98d36a633bcb90ddec238ffb2539 8755 tnseq-transit_3.3.12-1_arm64.buildinfo 01d57b26580a4c48fde098ca5460f32340ac781d 17574040 tnseq-transit_3.3.12-1_arm64.deb Checksums-Sha256: 46626c4c9e1adaae65c3fd661c28fe36d5d279d8f65ce1853201e05c4b707e8b 8755 tnseq-transit_3.3.12-1_arm64.buildinfo bb3b9d050fbb156d7d8563ae479cc883bc8b6872368da1a754067e97d605d08f 17574040 tnseq-transit_3.3.12-1_arm64.deb Files: a61771e4f0947bcb0e4f3a9b251ff320 8755 science optional tnseq-transit_3.3.12-1_arm64.buildinfo b444e804f239bd1329b177589513a3a0 17574040 science optional tnseq-transit_3.3.12-1_arm64.deb Thu Feb 6 10:41:03 UTC 2025 I: diffoscope 287 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_8-48013.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.zKecEb8X/tnseq-transit_3.3.12-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.zKecEb8X/tnseq-transit_3.3.12-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.zKecEb8X/tnseq-transit_3.3.12-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.zKecEb8X/b1/tnseq-transit_3.3.12-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.zKecEb8X/b2/tnseq-transit_3.3.12-1_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 diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 229ms CPU time consumed: 230ms Thu Feb 6 10:41:04 UTC 2025 I: diffoscope 287 found no differences in the changes files, and a .buildinfo file also exists. Thu Feb 6 10:41:04 UTC 2025 I: tnseq-transit from trixie built successfully and reproducibly on arm64. Thu Feb 6 10:41:05 UTC 2025 I: Submitting .buildinfo files to external archives: Thu Feb 6 10:41:05 UTC 2025 I: Submitting 12K b1/tnseq-transit_3.3.12-1_arm64.buildinfo.asc Thu Feb 6 10:41:06 UTC 2025 I: Submitting 12K b2/tnseq-transit_3.3.12-1_arm64.buildinfo.asc Thu Feb 6 10:41:07 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Feb 6 10:41:07 UTC 2025 I: Done submitting .buildinfo files. Thu Feb 6 10:41:07 UTC 2025 I: Removing signed tnseq-transit_3.3.12-1_arm64.buildinfo.asc files: removed './b1/tnseq-transit_3.3.12-1_arm64.buildinfo.asc' removed './b2/tnseq-transit_3.3.12-1_arm64.buildinfo.asc'