Wed Dec 18 02:02:32 UTC 2024 I: starting to build pigx-rnaseq/unstable/amd64 on jenkins on '2024-12-18 02:02' Wed Dec 18 02:02:32 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_14/26747/console.log Wed Dec 18 02:02:32 UTC 2024 I: Downloading source for unstable/pigx-rnaseq=0.1.1-1 --2024-12-18 02:02:32-- http://deb.debian.org/debian/pool/main/p/pigx-rnaseq/pigx-rnaseq_0.1.1-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2810 (2.7K) [text/prs.lines.tag] Saving to: ‘pigx-rnaseq_0.1.1-1.dsc’ 0K .. 100% 398M=0s 2024-12-18 02:02:32 (398 MB/s) - ‘pigx-rnaseq_0.1.1-1.dsc’ saved [2810/2810] Wed Dec 18 02:02:32 UTC 2024 I: pigx-rnaseq_0.1.1-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: pigx-rnaseq Binary: pigx-rnaseq Architecture: all Version: 0.1.1-1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Homepage: https://github.com/BIMSBbioinfo/pigx_rnaseq Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/pigx-rnaseq Vcs-Git: https://salsa.debian.org/med-team/pigx-rnaseq.git Build-Depends: debhelper-compat (= 13), autoconf-archive, fastp, fastqc , hisat2 , libjs-jquery-datatables , libjs-jquery-tablesorter , megadepth, multiqc, python3-all, python3-deeptools, python3-htseq, r-bioc-deseq2 , r-bioc-rtracklayer , r-bioc-summarizedexperiment , r-bioc-tximport , r-cran-corrplot , r-cran-crosstalk , r-cran-data.table , r-cran-dt , r-cran-ggplot2 , r-cran-ggrepel , r-cran-gprofiler2 , r-cran-ggpubr , r-cran-locfit , r-cran-pheatmap , r-cran-plotly , r-cran-reshape2 , r-cran-rjson , r-cran-rlang , r-cran-rmarkdown , r-cran-scales , salmon , samtools , snakemake , trim-galore Package-List: pigx-rnaseq deb science optional arch=all Checksums-Sha1: 0aea642e63d77ba02c7e5ce15ae23f9d0b9991fb 4423352 pigx-rnaseq_0.1.1.orig.tar.xz d91784423a6d062f117f3a03c33976427ff02064 15480 pigx-rnaseq_0.1.1-1.debian.tar.xz Checksums-Sha256: 4ecaee5321776fab24c36b0982ee80f5fefc38107ff885ceef9370b974b74cb0 4423352 pigx-rnaseq_0.1.1.orig.tar.xz 92a50fab9889042b3a216871d22b2668c14d6421bbe450f2a7d88f9f035c8c8a 15480 pigx-rnaseq_0.1.1-1.debian.tar.xz Files: 4843fa469087538a12397484788271f5 4423352 pigx-rnaseq_0.1.1.orig.tar.xz 0b3ce684c84e2301aa18ced7f62a42b4 15480 pigx-rnaseq_0.1.1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmbcP+UACgkQPCZ2P2xn 5uJ8GQ/+Oc1Uv6Tm4X7Ws6SpM713k+DLY97mvVdQ56UjygFQ+2+wipc1iCmITD4D As0N+URZD7HmX+gnIblInVQ9ZUdng7m8Mpj+wOjoahn7xcS1885LpB1QLQpsIZ1l QFELVQBbkuJP4mf/6jOyIb0ms48fbLYoc2HEMr/+TRL+4BxntkMJCyV9/E4lT4m9 7/mIntBKUYIyWNm3FCBtveKMr6qMPunz1yxPrBna7NEEqwKI7WZxAjP1qz1vesff ye/bLoFX3YCphQRBQOFdqY3ifec7W5/Rz7UO2VqkGue9j/3ed/KcB03GoKkjhiCh kvLVRHexDKm/mvncCqnJQc97ykIOu2soYnAUvo7p02PsmM86uIK1dch/AYvG+dI3 f6S1ibs/skQNDuI9Sr9INKNrvHZBsDmwzmibNpGmYtydDH6y+WhWK8qe88R3HRt7 1WtuTHmalv7o+0cg6VEEbf5M7kMR8H8B+89PusTxXsK0ZuVaavGV/oqVOdmoHI1v A02LCTpuaig/XaaUliVL63T2gl3wzj2Dzd0klVwYRne9kQO7HbN+Ut9HaXs4x3e5 KfmE4KfO7C7UWWkT2glz2UTP1xKlb9ToJecySbOHwIrKxzulMyPeTeOQ6TH6/Vxp fsso0lzvAiIwKVFB+LhvAQtO20+l7+Ku+vrpPqimh8QIDCEIzvM= =pIOt -----END PGP SIGNATURE----- Wed Dec 18 02:02:32 UTC 2024 I: Checking whether the package is not for us Wed Dec 18 02:02:32 UTC 2024 I: Starting 1st build on remote node ionos5-amd64.debian.net. Wed Dec 18 02:02:32 UTC 2024 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Wed Dec 18 02:08:15 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jan 19 20:25:34 -12 2026 I: pbuilder-time-stamp: 1768897534 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [pigx-rnaseq_0.1.1-1.dsc] I: copying [./pigx-rnaseq_0.1.1.orig.tar.xz] I: copying [./pigx-rnaseq_0.1.1-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Sep 7 11:58:29 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pigx-rnaseq_0.1.1-1.dsc: no acceptable signature found dpkg-source: info: extracting pigx-rnaseq in pigx-rnaseq-0.1.1 dpkg-source: info: unpacking pigx-rnaseq_0.1.1.orig.tar.xz dpkg-source: info: unpacking pigx-rnaseq_0.1.1-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1812173/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='0eabbf2b2dd54a259d504defc4db43d8' 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='1812173' 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.tTRzH070/pbuilderrc_rBzO --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tTRzH070/b1 --logfile b1/build.log pigx-rnaseq_0.1.1-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1812173/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), autoconf-archive, fastp, fastqc, hisat2, libjs-jquery-datatables, libjs-jquery-tablesorter, megadepth, multiqc, python3-all, python3-deeptools, python3-htseq, r-bioc-deseq2, r-bioc-rtracklayer, r-bioc-summarizedexperiment, r-bioc-tximport, r-cran-corrplot, r-cran-crosstalk, r-cran-data.table, r-cran-dt, r-cran-ggplot2, r-cran-ggrepel, r-cran-gprofiler2, r-cran-ggpubr, r-cran-locfit, r-cran-pheatmap, r-cran-plotly, r-cran-reshape2, r-cran-rjson, r-cran-rlang, r-cran-rmarkdown, r-cran-scales, salmon, samtools, snakemake, trim-galore dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19966 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 autoconf-archive; however: Package autoconf-archive is not installed. pbuilder-satisfydepends-dummy depends on fastp; however: Package fastp is not installed. pbuilder-satisfydepends-dummy depends on fastqc; however: Package fastqc is not installed. pbuilder-satisfydepends-dummy depends on hisat2; however: Package hisat2 is not installed. pbuilder-satisfydepends-dummy depends on libjs-jquery-datatables; however: Package libjs-jquery-datatables is not installed. pbuilder-satisfydepends-dummy depends on libjs-jquery-tablesorter; however: Package libjs-jquery-tablesorter is not installed. pbuilder-satisfydepends-dummy depends on megadepth; however: Package megadepth is not installed. pbuilder-satisfydepends-dummy depends on multiqc; however: Package multiqc is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-deeptools; however: Package python3-deeptools is not installed. pbuilder-satisfydepends-dummy depends on python3-htseq; however: Package python3-htseq is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-deseq2; however: Package r-bioc-deseq2 is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-rtracklayer; however: Package r-bioc-rtracklayer is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-summarizedexperiment; however: Package r-bioc-summarizedexperiment is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-tximport; however: Package r-bioc-tximport is not installed. pbuilder-satisfydepends-dummy depends on r-cran-corrplot; however: Package r-cran-corrplot is not installed. pbuilder-satisfydepends-dummy depends on r-cran-crosstalk; however: Package r-cran-crosstalk is not installed. pbuilder-satisfydepends-dummy depends on r-cran-data.table; however: Package r-cran-data.table is not installed. pbuilder-satisfydepends-dummy depends on r-cran-dt; however: Package r-cran-dt is not installed. pbuilder-satisfydepends-dummy depends on r-cran-ggplot2; however: Package r-cran-ggplot2 is not installed. pbuilder-satisfydepends-dummy depends on r-cran-ggrepel; however: Package r-cran-ggrepel is not installed. pbuilder-satisfydepends-dummy depends on r-cran-gprofiler2; however: Package r-cran-gprofiler2 is not installed. pbuilder-satisfydepends-dummy depends on r-cran-ggpubr; however: Package r-cran-ggpubr is not installed. pbuilder-satisfydepends-dummy depends on r-cran-locfit; however: Package r-cran-locfit is not installed. pbuilder-satisfydepends-dummy depends on r-cran-pheatmap; however: Package r-cran-pheatmap is not installed. pbuilder-satisfydepends-dummy depends on r-cran-plotly; however: Package r-cran-plotly is not installed. pbuilder-satisfydepends-dummy depends on r-cran-reshape2; however: Package r-cran-reshape2 is not installed. pbuilder-satisfydepends-dummy depends on r-cran-rjson; however: Package r-cran-rjson is not installed. pbuilder-satisfydepends-dummy depends on r-cran-rlang; however: Package r-cran-rlang is not installed. pbuilder-satisfydepends-dummy depends on r-cran-rmarkdown; however: Package r-cran-rmarkdown is not installed. pbuilder-satisfydepends-dummy depends on r-cran-scales; however: Package r-cran-scales is not installed. pbuilder-satisfydepends-dummy depends on salmon; however: Package salmon is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on snakemake; however: Package snakemake is not installed. pbuilder-satisfydepends-dummy depends on trim-galore; however: Package trim-galore 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: adwaita-icon-theme{a} at-spi2-common{a} autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} coinor-cbc{a} coinor-libcbc3.1{a} coinor-libcgl1{a} coinor-libclp1{a} coinor-libcoinutils3v5{a} coinor-libosi1v5{a} cutadapt{a} dbus{a} dbus-bin{a} dbus-daemon{a} dbus-session-bus-common{a} dbus-system-bus-common{a} dbus-user-session{a} dconf-gsettings-backend{a} dconf-service{a} debhelper{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} fastp{a} fastqc{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-font-awesome{a} fonts-glyphicons-halflings{a} fonts-lyx{a} fonts-mathjax{a} gettext{a} gettext-base{a} git{a} git-man{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} hisat2{a} intltool-debian{a} java-common{a} javascript-common{a} libapache-pom-java{a} libapparmor1{a} libarchive-zip-perl{a} libasound2-data{a} libasound2t64{a} libatk-bridge2.0-0t64{a} libatk1.0-0t64{a} libatspi2.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbigwig0t64{a} libblas3{a} libboost-dev{a} libboost-filesystem1.83.0{a} libboost-program-options1.83.0{a} libboost1.83-dev{a} libbrotli1{a} libcairo-gobject2{a} libcairo2{a} libcloudproviders0{a} libcolord2{a} libcom-err2{a} libcommons-codec-java{a} libcommons-compress-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-logging-java{a} libcommons-math3-java{a} libcommons-parent-java{a} libcups2t64{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdatrie1{a} libdbus-1-3{a} libdconf1{a} libdebhelper-perl{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} 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libxi6{a} libxinerama1{a} libxkbcommon0{a} libxml2{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxslt1.1{a} libxss1{a} libxt6t64{a} libxtst6{a} libxxf86vm1{a} libyaml-0-2{a} libz3-4{a} littler{a} m4{a} man-db{a} media-types{a} megadepth{a} mesa-libgallium{a} multiqc{a} ncbi-vdb-data{a} netbase{a} node-bootstrap-sass{a} node-html5shiv{a} node-normalize.css{a} openjdk-21-jre{a} openjdk-21-jre-headless{a} openssl{a} pandoc{a} pandoc-data{a} pigz{a} po-debconf{a} procps{a} python-babel-localedata{a} python-matplotlib-data{a} python3{a} python3-alabaster{a} python3-all{a} python3-attr{a} python3-autocommand{a} python3-babel{a} python3-brotli{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-click{a} python3-colorama{a} python3-coloredlogs{a} python3-colormath{a} python3-configargparse{a} python3-connection-pool{a} python3-contourpy{a} python3-cutadapt{a} python3-cycler{a} python3-dateutil{a} python3-datrie{a} python3-decorator{a} python3-deeptools{a} python3-deeptoolsintervals{a} python3-defusedxml{a} python3-dnaio{a} python3-docutils{a} python3-dpath{a} python3-fastjsonschema{a} python3-fonttools{a} python3-fs{a} python3-git{a} python3-gitdb{a} python3-htseq{a} python3-humanfriendly{a} python3-humanize{a} python3-idna{a} python3-imagesize{a} python3-importlib-metadata{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jinja2{a} python3-jsonschema{a} python3-jsonschema-specifications{a} python3-jupyter-core{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-lzstring{a} python3-markdown{a} python3-markdown-it{a} python3-markupsafe{a} python3-matplotlib{a} python3-mdurl{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-nbformat{a} python3-networkx{a} python3-numpy{a} python3-numpydoc{a} python3-packaging{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-plac{a} python3-platformdirs{a} python3-plotly{a} python3-psutil{a} python3-pulp{a} python3-py{a} python3-py2bit{a} python3-pyaml-env{a} python3-pybigwig{a} python3-pygments{a} python3-pyparsing{a} python3-pysam{a} python3-ratelimiter{a} python3-referencing{a} python3-requests{a} python3-retry{a} python3-rich{a} python3-rich-click{a} python3-roman{a} python3-rpds-py{a} python3-scipy{a} python3-smart-open{a} python3-smmap{a} python3-snowballstemmer{a} python3-spectra{a} python3-sphinx{a} python3-stopit{a} python3-sympy{a} python3-tabulate{a} python3-tenacity{a} python3-throttler{a} python3-tk{a} python3-toposort{a} python3-traitlets{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-unicodedata2{a} python3-urllib3{a} python3-wrapt{a} python3-xopen{a} python3-yaml{a} python3-yte{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} python3.12-tk{a} python3.13{a} python3.13-minimal{a} python3.13-tk{a} r-base-core{a} r-bioc-biobase{a} r-bioc-biocgenerics{a} r-bioc-biocio{a} r-bioc-biocparallel{a} r-bioc-biostrings{a} r-bioc-delayedarray{a} r-bioc-deseq2{a} r-bioc-genomeinfodb{a} r-bioc-genomeinfodbdata{a} r-bioc-genomicalignments{a} r-bioc-genomicranges{a} r-bioc-iranges{a} r-bioc-matrixgenerics{a} r-bioc-rhtslib{a} r-bioc-rsamtools{a} r-bioc-rtracklayer{a} r-bioc-s4arrays{a} r-bioc-s4vectors{a} r-bioc-sparsearray{a} r-bioc-summarizedexperiment{a} r-bioc-tximport{a} r-bioc-ucsc.utils{a} r-bioc-xvector{a} r-bioc-zlibbioc{a} r-cran-abind{a} r-cran-askpass{a} r-cran-backports{a} r-cran-base64enc{a} r-cran-bh{a} r-cran-bit{a} r-cran-bit64{a} r-cran-bitops{a} r-cran-boot{a} r-cran-broom{a} r-cran-bslib{a} r-cran-cachem{a} r-cran-car{a} r-cran-cardata{a} r-cran-caret{a} r-cran-cellranger{a} r-cran-class{a} r-cran-cli{a} r-cran-clipr{a} r-cran-clock{a} r-cran-codetools{a} r-cran-colorspace{a} r-cran-colourpicker{a} r-cran-commonmark{a} r-cran-conquer{a} r-cran-corrplot{a} r-cran-cowplot{a} r-cran-cpp11{a} r-cran-crayon{a} r-cran-crosstalk{a} r-cran-curl{a} r-cran-data.table{a} r-cran-deriv{a} r-cran-diagram{a} r-cran-digest{a} r-cran-doby{a} r-cran-dplyr{a} r-cran-dt{a} r-cran-e1071{a} r-cran-ellipsis{a} r-cran-evaluate{a} r-cran-fansi{a} r-cran-farver{a} r-cran-fastmap{a} r-cran-fontawesome{a} r-cran-forcats{a} r-cran-foreach{a} r-cran-foreign{a} r-cran-formatr{a} r-cran-formula{a} r-cran-fs{a} r-cran-futile.logger{a} r-cran-futile.options{a} r-cran-future{a} r-cran-future.apply{a} r-cran-generics{a} r-cran-ggplot2{a} r-cran-ggpubr{a} r-cran-ggrepel{a} r-cran-ggsci{a} r-cran-ggsignif{a} r-cran-globals{a} r-cran-glue{a} r-cran-gower{a} r-cran-gprofiler2{a} r-cran-gridextra{a} r-cran-gtable{a} r-cran-hardhat{a} r-cran-haven{a} r-cran-highr{a} r-cran-hms{a} r-cran-htmltools{a} r-cran-htmlwidgets{a} r-cran-httpuv{a} r-cran-httr{a} r-cran-ipred{a} r-cran-isoband{a} r-cran-iterators{a} r-cran-jquerylib{a} r-cran-jsonlite{a} r-cran-kernsmooth{a} r-cran-knitr{a} r-cran-labeling{a} r-cran-lambda.r{a} r-cran-later{a} r-cran-lattice{a} r-cran-lava{a} r-cran-lazyeval{a} r-cran-lifecycle{a} r-cran-listenv{a} r-cran-littler{a} r-cran-lme4{a} r-cran-locfit{a} r-cran-lubridate{a} r-cran-magrittr{a} r-cran-mass{a} r-cran-matrix{a} r-cran-matrixmodels{a} r-cran-matrixstats{a} r-cran-memoise{a} r-cran-mgcv{a} r-cran-microbenchmark{a} r-cran-mime{a} r-cran-miniui{a} r-cran-minqa{a} r-cran-modelmetrics{a} r-cran-modelr{a} r-cran-munsell{a} r-cran-nlme{a} r-cran-nloptr{a} r-cran-nnet{a} r-cran-numderiv{a} r-cran-openssl{a} r-cran-openxlsx{a} r-cran-parallelly{a} r-cran-pbkrtest{a} r-cran-pheatmap{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-pkgkitten{a} r-cran-plotly{a} r-cran-plyr{a} r-cran-polynom{a} r-cran-prettyunits{a} r-cran-proc{a} r-cran-prodlim{a} r-cran-progress{a} r-cran-progressr{a} r-cran-promises{a} r-cran-proxy{a} r-cran-purrr{a} r-cran-quantreg{a} r-cran-r.methodss3{a} r-cran-r.oo{a} r-cran-r.utils{a} r-cran-r6{a} r-cran-rappdirs{a} r-cran-rcolorbrewer{a} r-cran-rcpp{a} r-cran-rcpparmadillo{a} r-cran-rcppeigen{a} r-cran-rcurl{a} r-cran-readr{a} r-cran-readxl{a} r-cran-recipes{a} r-cran-rematch{a} r-cran-reshape2{a} r-cran-restfulr{a} r-cran-rio{a} r-cran-rjson{a} r-cran-rlang{a} r-cran-rmarkdown{a} r-cran-rpart{a} r-cran-rstatix{a} r-cran-sass{a} r-cran-scales{a} r-cran-shape{a} r-cran-shiny{a} r-cran-shinyjs{a} r-cran-snow{a} r-cran-sourcetools{a} r-cran-sparsem{a} r-cran-squarem{a} r-cran-statmod{a} r-cran-stringi{a} r-cran-stringr{a} r-cran-survival{a} r-cran-sys{a} r-cran-tibble{a} r-cran-tidyr{a} r-cran-tidyselect{a} r-cran-timechange{a} r-cran-timedate{a} r-cran-tinytex{a} r-cran-tzdb{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{a} r-cran-vroom{a} r-cran-withr{a} r-cran-writexl{a} r-cran-xfun{a} r-cran-xml{a} r-cran-xtable{a} r-cran-yaml{a} r-cran-zip{a} readline-common{a} salmon{a} samtools{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} snakemake{a} sphinx-common{a} systemd{a} systemd-sysv{a} tk8.6-blt2.5{a} trim-galore{a} tzdata{a} ucf{a} unicode-data{a} unzip{a} x11-common{a} xdg-utils{a} xkb-data{a} xml-core{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf at-spi2-core bcftools chromium chrony curl cwltool dillo edbrowse elinks epiphany-browser falkon firefox firefox-esr fonts-dejavu-extra graphicsmagick-imagemagick-compat imagemagick imagemagick-6.q16 imagemagick-7.q16 isympy-common konqueror krb5-locales less libarchive-cpio-perl libatk-wrapper-java-jni libfile-mimeinfo-perl libgdk-pixbuf2.0-bin libglib2.0-data libgpm2 libgtk-3-bin libhwloc-plugins libjs-filesaver libjson-xs-perl libkmod2 libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libnss-systemd librsvg2-common libsasl2-modules libx11-protocol-perl links links2 linux-sysctl-defaults luakit lynx mesa-vulkan-drivers morph-browser netrik netsurf-fb netsurf-gtk node-clipboard node-highlight.js node-jquery ntpsec openntpd openssh-client privacybrowser psmisc publicsuffix python3-azure-storage python3-biopython python3-boto3 python3-botocore python3-bs4 python3-cssselect python3-dropbox python3-flask python3-ftputil python3-gdal python3-hisat2 python3-html5lib python3-irodsclient python3-json-pointer python3-kubernetes python3-olefile python3-paramiko python3-pooch python3-pydot python3-pygraphviz python3-rfc3987 python3-uritemplate python3-webcolors python3-yappi python3-zstandard qutebrowser r-base-dev r-bioc-graph r-cran-aer r-cran-bbmle r-cran-bench r-cran-bookdown r-cran-brio r-cran-cairo r-cran-callr r-cran-cba r-cran-cluster r-cran-cmprsk r-cran-coda r-cran-coin r-cran-covr r-cran-dbi r-cran-dbplyr r-cran-ddalpha r-cran-decor r-cran-dendextend r-cran-desc r-cran-devtools r-cran-dials r-cran-dichromat r-cran-dimred r-cran-doparallel r-cran-downlit r-cran-dygraphs r-cran-earth r-cran-ellipse r-cran-emmeans r-cran-epir r-cran-fastica r-cran-fields r-cran-formattable r-cran-furrr r-cran-gam r-cran-gee r-cran-geepack r-cran-ggalluvial r-cran-ggally r-cran-ggbeeswarm r-cran-ggthemes r-cran-glmnet r-cran-gmm r-cran-gridgraphics r-cran-gridsvg r-cran-hexbin r-cran-hmisc r-cran-igraph r-cran-interp r-cran-irdisplay r-cran-irlba r-cran-itertools r-cran-jpeg r-cran-kernlab r-cran-ks r-cran-lavaan r-cran-lavasearch2 r-cran-leaps r-cran-lintr r-cran-lmtest r-cran-lobstr r-cran-logcondens r-cran-lsmeans r-cran-magick r-cran-mapproj r-cran-maps r-cran-markdown r-cran-mclust r-cran-mda r-cran-metafor r-cran-mets r-cran-mlbench r-cran-mlmetrics r-cran-mockery r-cran-mockr r-cran-modeldata r-cran-multcomp r-cran-mvtnorm r-cran-network r-cran-optimx r-cran-ordinal r-cran-palmerpenguins r-cran-party r-cran-patchwork r-cran-pbmcapply r-cran-pkgdown r-cran-pkgload r-cran-plm r-cran-png r-cran-polycor r-cran-processx r-cran-profvis r-cran-ps r-cran-psych r-cran-r.devices r-cran-r.rsp r-cran-ragg r-cran-randomforest r-cran-rann r-cran-rcppml r-cran-rcpproll r-cran-remotes r-cran-renv r-cran-reticulate r-cran-rgl r-cran-rhpcblasctl r-cran-rmysql r-cran-robust r-cran-robustbase r-cran-roxygen2 r-cran-rpostgresql r-cran-rprojroot r-cran-rsample r-cran-rsconnect r-cran-rspectra r-cran-rsqlite r-cran-rstudioapi r-cran-rsvg r-cran-runit r-cran-rversions r-cran-sandwich r-cran-seriation r-cran-setrng r-cran-sf r-cran-slider r-cran-sodium r-cran-spatialreg r-cran-spdep r-cran-spelling r-cran-splines2 r-cran-survey r-cran-svglite r-cran-systemfit r-cran-testit r-cran-testthat r-cran-th.data r-cran-thematic r-cran-themis r-cran-tidyverse r-cran-tikzdevice r-cran-tseries r-cran-unitizer r-cran-usethis r-cran-vcd r-cran-vdiffr r-cran-venndiagram r-cran-viridis r-cran-waldo r-cran-webshot r-cran-webutils r-cran-whoami r-cran-xml2 r-cran-xts r-cran-zeallot r-cran-zoo r-doc-html r-recommended sugar-browse-activity surf systemd-cryptsetup systemd-timesyncd texlive-xetex vimb w3m wget x11-utils x11-xserver-utils xdg-user-dirs xemacs21-mule xemacs21-mule-canna-wnn xemacs21-nomule 0 packages upgraded, 657 newly installed, 0 to remove and 0 not upgraded. Need to get 582 MB of archives. After unpacking 2209 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libapparmor1 amd64 3.1.7-1+b3 [42.1 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libsystemd-shared amd64 257-2 [2136 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 systemd amd64 257-2 [3608 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 systemd-sysv amd64 257-2 [59.6 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.16.0-1 [177 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 dbus-bin amd64 1.16.0-1 [78.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 dbus-session-bus-common all 1.16.0-1 [51.1 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 dbus-daemon amd64 1.16.0-1 [157 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 dbus-system-bus-common all 1.16.0-1 [52.2 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 dbus amd64 1.16.0-1 [70.5 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf-archive all 20220903-3 [775 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 pigz amd64 2.8-1 [62.7 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.8-3 [817 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.8-3 [2162 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-4 [256 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2~rc1-2 [23.8 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 24 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.8-3 [1969 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.8-3 [677 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get: 34 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.1-2 [858 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.1-2 [2198 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-3 [200 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-6 [1184 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libpam-systemd amd64 257-2 [292 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-12 [92.0 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0045 [45.2 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.4-1 [1501 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-5+b1 [759 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.44-3 [280 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1+b1 [141 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 gtk-update-icon-cache amd64 4.16.7+ds-1 [50.2 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 adwaita-icon-theme all 47.0-2 [463 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 at-spi2-common all 2.54.0-1 [170 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-3 [723 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b3 [27.8 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b3 [54.6 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get: 97 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-11 [836 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 coinor-libcoinutils3v5 amd64 2.11.11+ds-2 [458 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 coinor-libosi1v5 amd64 0.108.10+ds-1+b1 [293 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 coinor-libclp1 amd64 1.17.10+ds-1 [883 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 coinor-libcgl1 amd64 0.60.9+ds-1 [426 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 coinor-libcbc3.1 amd64 2.10.12+ds-1 [714 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 coinor-cbc amd64 2.10.12+ds-1 [16.2 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 python3-importlib-metadata all 8.5.0-1 [21.0 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 115 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 python3-xopen all 1.7.0-2 [16.9 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 python3-dnaio amd64 1.2.3-1 [101 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 python3-cutadapt amd64 4.7-2+b2 [241 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 cutadapt all 4.7-2 [25.1 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 dbus-user-session amd64 1.16.0-1 [51.0 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libdconf1 amd64 0.40.0-4+b3 [41.9 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 dconf-service amd64 0.40.0-4+b3 [32.6 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 dconf-gsettings-backend amd64 0.40.0-4+b3 [28.8 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.21 [88.9 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 131 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-3 [1600 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.21 [919 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 java-common all 0.76 [6776 B] Get: 138 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.36-1 [110 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.106-1 [1392 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.3.0-3 [55.8 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jre-headless amd64 21.0.5+11-1 [41.8 MB] Get: 143 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get: 144 http://deb.debian.org/debian unstable/main amd64 libatk1.0-0t64 amd64 2.54.0-1 [51.2 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libatspi2.0-0t64 amd64 2.54.0-1 [76.4 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libatk-bridge2.0-0t64 amd64 2.54.0-1 [67.6 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libcloudproviders0 amd64 0.3.6-1+b1 [29.2 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libcolord2 amd64 1.4.7-1+b2 [140 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-15 [112 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-15 [44.1 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-15 [48.1 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-2 [251 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.1.0-1 [478 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.55.0+ds-3 [225 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.55.0+ds-3 [54.6 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.55.0+ds-3 [35.4 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libwayland-client0 amd64 1.23.0-1+b1 [26.6 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libwayland-cursor0 amd64 1.23.0-1+b1 [11.7 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libwayland-egl1 amd64 1.23.0-1+b1 [5664 B] Get: 173 http://deb.debian.org/debian unstable/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b3 [20.2 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libxcursor1 amd64 1:1.2.2-1+b1 [37.6 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libxinerama1 amd64 2:1.1.4-3+b3 [16.0 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 xkb-data all 2.42-1 [790 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libxkbcommon0 amd64 1.7.0-2 [113 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libxrandr2 amd64 2:1.5.4-1+b2 [36.4 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libgtk-3-common all 3.24.43-4 [4657 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libgtk-3-0t64 amd64 3.24.43-4 [2754 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 185 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libglapi-mesa amd64 24.2.8-1 [38.0 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 libxcb-dri2-0 amd64 1.17.0-2+b1 [107 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b2 [8848 B] Get: 196 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b3 [19.3 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b2 [51.9 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.5-1 [26.0 MB] Get: 204 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 mesa-libgallium amd64 24.2.8-1 [9185 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.3.296.0-1 [126 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libwayland-server0 amd64 1.23.0-1+b1 [34.2 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libgbm1 amd64 24.2.8-1 [42.8 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 24.2.8-1 [43.9 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 24.2.8-1 [154 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 libasound2-data all 1.2.12-1 [21.0 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 libasound2t64 amd64 1.2.12-1+b1 [371 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libxtst6 amd64 2:1.2.3-1.1+b3 [25.9 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jre amd64 21.0.5+11-1 [205 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 default-jre amd64 2:1.21-76 [1068 B] Get: 220 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libisal2 amd64 2.31.0-0.3 [114 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 fastp amd64 0.23.4+dfsg-1 [203 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 libjbzip2-java all 0.9.1-8 [42.7 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 227 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 libcommons-codec-java all 1.17.1-1 [303 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 libcommons-io-java all 2.17.0-1 [488 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 libmjson-java all 1.4.0-3 [60.4 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1189 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 libncbi-ngs3 amd64 3.0.9+dfsg-7+b1 [157 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 libngs-jni amd64 3.0.9+dfsg-7+b1 [25.8 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 libngs-java amd64 3.0.9+dfsg-7+b1 [112 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 librhino-java all 1.7.15-1 [1382 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 libsnappy-jni amd64 1.1.10.7-1 [6492 B] Get: 245 http://deb.debian.org/debian unstable/main amd64 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 libhtsjdk-java all 4.1.0+dfsg-2 [1833 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 libfindbin-libs-perl all 3.0.2-1 [29.7 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 fastqc all 0.12.1+dfsg-4 [398 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.2.1-1 [190 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.11.1-1 [360 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 liberror-perl all 0.17029-2 [29.0 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 git-man all 1:2.45.2-1.2 [2159 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 git amd64 1:2.45.2-1.2 [8662 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 hisat2 amd64 2.2.1-5 [3702 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 javascript-common all 11+nmu1 [6260 B] Get: 269 http://deb.debian.org/debian unstable/main amd64 libbigwig0t64 amd64 0.4.7+dfsg-3.1+b2 [28.7 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-4 [10.6 MB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 272 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-4 [282 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4 [347 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.1-1 [351 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.11.2-1 [164 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 libjemalloc2 amd64 5.3.0-2+b2 [275 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 libjs-popper.js all 1.16.1+ds-6 [52.4 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [517 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 libjs-d3 all 3.5.17-4 [132 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 libjs-es5-shim all 4.6.7-2 [47.4 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [397 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [144 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-datatables-extensions all 0.0+git20150910.28fd64e+dfsg-5 [648 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-metadata all 12-4 [6532 B] Get: 291 http://deb.debian.org/debian unstable/main amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.2 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3672 B] Get: 293 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [52.1 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [184 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 libjs-json all 0~20221030+~1.0.8-1 [20.0 kB] Get: 297 http://deb.debian.org/debian unstable/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 298 http://deb.debian.org/debian unstable/main amd64 libjs-modernizr all 3.13.0-0.1 [191 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 libjs-prettify all 2015.12.04+dfsg-1.1 [41.7 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 301 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-2 [30.3 kB] Get: 302 http://deb.debian.org/debian unstable/main amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [32.1 kB] Get: 303 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 304 http://deb.debian.org/debian unstable/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get: 305 http://deb.debian.org/debian unstable/main amd64 liblua5.4-0 amd64 5.4.7-1+b1 [147 kB] Get: 306 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 libnlopt0 amd64 2.7.1-6+b1 [178 kB] Get: 308 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get: 309 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get: 310 http://deb.debian.org/debian unstable/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get: 311 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get: 312 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.8-3 [2154 kB] Get: 313 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.1-2 [1975 kB] Get: 314 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.1-2 [2151 kB] Get: 315 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get: 316 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get: 317 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 318 http://deb.debian.org/debian unstable/main amd64 libstaden-read14t64 amd64 1.15.0-1.1+b2 [268 kB] Get: 319 http://deb.debian.org/debian unstable/main amd64 libtbbmalloc2 amd64 2021.12.0-1 [48.9 kB] Get: 320 http://deb.debian.org/debian unstable/main amd64 libtbbbind-2-5 amd64 2021.12.0-1 [14.4 kB] Get: 321 http://deb.debian.org/debian unstable/main amd64 libtbb12 amd64 2021.12.0-1 [87.8 kB] Get: 322 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 323 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.4.0-0.1+b1 [111 kB] Get: 324 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB] Get: 325 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get: 326 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get: 327 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB] Get: 328 http://deb.debian.org/debian unstable/main amd64 zip amd64 3.0-14 [233 kB] Get: 329 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB] Get: 330 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 331 http://deb.debian.org/debian unstable/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get: 332 http://deb.debian.org/debian unstable/main amd64 r-cran-littler amd64 0.3.20-2 [103 kB] Get: 333 http://deb.debian.org/debian unstable/main amd64 littler all 0.3.20-2 [16.0 kB] Get: 334 http://deb.debian.org/debian unstable/main amd64 megadepth amd64 1.2.0-4+b1 [83.0 kB] Get: 335 http://deb.debian.org/debian unstable/main amd64 python3-colorama all 0.4.6-4 [36.2 kB] Get: 336 http://deb.debian.org/debian unstable/main amd64 python3-click all 8.1.7-2 [94.3 kB] Get: 337 http://deb.debian.org/debian unstable/main amd64 python3-humanfriendly all 10.0-6 [85.6 kB] Get: 338 http://deb.debian.org/debian unstable/main amd64 python3-coloredlogs all 15.0.1-1 [47.4 kB] Get: 339 http://deb.debian.org/debian unstable/main amd64 python3-humanize all 4.11.0-1 [52.7 kB] Get: 340 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b2 [13.9 kB] Get: 341 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.3-1.1 [120 kB] Get: 342 http://deb.debian.org/debian unstable/main amd64 python3-markdown all 3.7-2 [85.2 kB] Get: 343 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 344 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 345 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 10.4.0-1+b1 [522 kB] Get: 346 http://deb.debian.org/debian unstable/main amd64 python3.12-tk amd64 3.12.8-3 [113 kB] Get: 347 http://deb.debian.org/debian unstable/main amd64 python3.13-tk amd64 3.13.1-2 [103 kB] Get: 348 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.13.1-1 [9464 B] Get: 349 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 10.4.0-1+b1 [79.8 kB] Get: 350 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 351 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB] Get: 352 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.3.1-1 [264 kB] Get: 353 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get: 354 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b6 [321 kB] Get: 355 http://deb.debian.org/debian unstable/main amd64 python3-tz all 2024.2-1 [31.0 kB] Get: 356 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 357 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-5.1 [95.2 kB] Get: 358 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 5.3.0-1+b1 [1676 kB] Get: 359 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.4.0+dfsg-1 [25.5 kB] Get: 360 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 361 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.14.1-3 [20.5 MB] Get: 362 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 363 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.13.3-1 [4147 kB] Get: 364 http://deb.debian.org/debian unstable/main amd64 python3-attr all 24.2.0-1 [68.4 kB] Get: 365 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB] Get: 366 http://deb.debian.org/debian unstable/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b3 [299 kB] Get: 367 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.1-2 [740 kB] Get: 368 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.12.7-1 [1052 B] Get: 369 http://deb.debian.org/debian unstable/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get: 370 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.55.0-3 [1634 kB] Get: 371 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.7-2+b1 [77.0 kB] Get: 372 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 373 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.8.3-3+b1 [5654 kB] Get: 374 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 375 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB] Get: 376 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.8-2 [41.6 kB] Get: 377 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.2.3-4 [112 kB] Get: 378 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 379 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 380 http://deb.debian.org/debian unstable/main amd64 python3-fastjsonschema all 2.20.0-1 [21.8 kB] Get: 381 http://deb.debian.org/debian unstable/main amd64 python3-rpds-py amd64 0.21.0-2 [287 kB] Get: 382 http://deb.debian.org/debian unstable/main amd64 python3-referencing all 0.35.1-2 [23.5 kB] Get: 383 http://deb.debian.org/debian unstable/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get: 384 http://deb.debian.org/debian unstable/main amd64 python3-jsonschema all 4.19.2-5 [71.4 kB] Get: 385 http://deb.debian.org/debian unstable/main amd64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB] Get: 386 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-core all 5.7.2-5 [35.3 kB] Get: 387 http://deb.debian.org/debian unstable/main amd64 python3-nbformat all 5.9.1-1 [45.1 kB] Get: 388 http://deb.debian.org/debian unstable/main amd64 python3-tenacity all 8.4.2+really8.4.1-1 [46.0 kB] Get: 389 http://deb.debian.org/debian unstable/main amd64 python3-plotly all 5.20.0+dfsg-1 [2726 kB] Get: 390 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-1+b1 [178 kB] Get: 391 http://deb.debian.org/debian unstable/main amd64 python3-pyaml-env all 1.2.1-2 [9032 B] Get: 392 http://deb.debian.org/debian unstable/main amd64 python3-mdurl all 0.1.2-1 [9444 B] Get: 393 http://deb.debian.org/debian unstable/main amd64 python3-markdown-it all 3.0.0-2 [62.5 kB] Get: 394 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 395 http://deb.debian.org/debian unstable/main amd64 python3-rich all 13.7.1-1 [201 kB] Get: 396 http://deb.debian.org/debian unstable/main amd64 python3-rich-click all 1.6.0-1 [20.8 kB] Get: 397 http://deb.debian.org/debian unstable/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 398 http://deb.debian.org/debian unstable/main amd64 python3-colormath all 3.0.0-4 [34.7 kB] Get: 399 http://deb.debian.org/debian unstable/main amd64 python3-spectra all 0.0.11-4 [16.5 kB] Get: 400 http://deb.debian.org/debian unstable/main amd64 python3-lzstring all 1.0.4-3 [5544 B] Get: 401 http://deb.debian.org/debian unstable/main amd64 multiqc all 1.21+dfsg-2 [781 kB] Get: 402 http://deb.debian.org/debian unstable/main amd64 node-bootstrap-sass all 3.4.3-2 [186 kB] Get: 403 http://deb.debian.org/debian unstable/main amd64 node-html5shiv all 3.7.3+dfsg-5 [13.2 kB] Get: 404 http://deb.debian.org/debian unstable/main amd64 node-normalize.css all 8.0.1-5 [12.7 kB] Get: 405 http://deb.debian.org/debian unstable/main amd64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 406 http://deb.debian.org/debian unstable/main amd64 pandoc amd64 3.1.11.1+ds-2 [26.4 MB] Get: 407 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.16.0-1 [5696 kB] Get: 408 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 409 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.16.0-1 [114 kB] Get: 410 http://deb.debian.org/debian unstable/main amd64 python3-configargparse all 1.7-2 [31.4 kB] Get: 411 http://deb.debian.org/debian unstable/main amd64 python3-connection-pool all 0.0.3-2 [5584 B] Get: 412 http://deb.debian.org/debian unstable/main amd64 python3-datrie amd64 0.8.2-5+b1 [174 kB] Get: 413 http://deb.debian.org/debian unstable/main amd64 python3-deeptoolsintervals amd64 0.1.9-3+b10 [51.3 kB] Get: 414 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 415 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 8.1.3-2 [616 kB] Get: 416 http://deb.debian.org/debian unstable/main amd64 python3-roman all 4.2-1 [10.4 kB] Get: 417 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 418 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 419 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 420 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 8.1.3-2 [468 kB] Get: 421 http://deb.debian.org/debian unstable/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB] Get: 422 http://deb.debian.org/debian unstable/main amd64 python3-numpydoc all 1.8.0-1 [51.4 kB] Get: 423 http://deb.debian.org/debian unstable/main amd64 python3-py2bit amd64 0.3.2-1 [19.2 kB] Get: 424 http://deb.debian.org/debian unstable/main amd64 python3-pybigwig amd64 0.3.23+dfsg-1+b1 [39.5 kB] Get: 425 http://deb.debian.org/debian unstable/main amd64 python3-pysam amd64 0.22.1+ds-2+b2 [4412 kB] Get: 426 http://deb.debian.org/debian unstable/main amd64 python3-deeptools all 3.5.5+dfsg-1 [149 kB] Get: 427 http://deb.debian.org/debian unstable/main amd64 python3-dpath all 2.2.0-1 [19.9 kB] Get: 428 http://deb.debian.org/debian unstable/main amd64 python3-smmap all 6.0.0-1 [20.1 kB] Get: 429 http://deb.debian.org/debian unstable/main amd64 python3-gitdb all 4.0.11-1 [45.5 kB] Get: 430 http://deb.debian.org/debian unstable/main amd64 python3-git all 3.1.37-3 [137 kB] Get: 431 http://deb.debian.org/debian unstable/main amd64 python3-htseq amd64 2.0.9+dfsg-1 [438 kB] Get: 432 http://deb.debian.org/debian unstable/main amd64 python3-plac all 1.4.3-2 [65.7 kB] Get: 433 http://deb.debian.org/debian unstable/main amd64 python3-psutil amd64 5.9.8-2 [225 kB] Get: 434 http://deb.debian.org/debian unstable/main amd64 python3-pulp all 2.7.0+dfsg-4 [72.4 kB] Get: 435 http://deb.debian.org/debian unstable/main amd64 python3-py all 1.11.0-2 [88.7 kB] Get: 436 http://deb.debian.org/debian unstable/main amd64 python3-ratelimiter amd64 1.2.0.post0-4 [5740 B] Get: 437 http://deb.debian.org/debian unstable/main amd64 python3-retry all 0.9.2-3 [7088 B] Get: 438 http://deb.debian.org/debian unstable/main amd64 python3-wrapt amd64 1.15.0-3+b1 [43.8 kB] Get: 439 http://deb.debian.org/debian unstable/main amd64 python3-smart-open all 7.1.0-1 [98.7 kB] Get: 440 http://deb.debian.org/debian unstable/main amd64 python3-stopit all 1.1.2-3 [12.8 kB] Get: 441 http://deb.debian.org/debian unstable/main amd64 python3-throttler all 1.2.2-2 [7072 B] Get: 442 http://deb.debian.org/debian unstable/main amd64 python3-toposort all 1.10-2 [7336 B] Get: 443 http://deb.debian.org/debian unstable/main amd64 python3-yte all 1.5.4-1 [13.6 kB] Get: 444 http://deb.debian.org/debian unstable/main amd64 r-bioc-biocgenerics all 0.50.0-2 [607 kB] Get: 445 http://deb.debian.org/debian unstable/main amd64 r-bioc-biobase amd64 2.64.0-4 [2132 kB] Get: 446 http://deb.debian.org/debian unstable/main amd64 r-bioc-s4vectors amd64 0.42.1+dfsg-2 [1894 kB] Get: 447 http://deb.debian.org/debian unstable/main amd64 r-bioc-biocio all 1.14.0+dfsg-1 [210 kB] Get: 448 http://deb.debian.org/debian unstable/main amd64 r-cran-formatr all 1.14-2 [152 kB] Get: 449 http://deb.debian.org/debian unstable/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get: 450 http://deb.debian.org/debian unstable/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get: 451 http://deb.debian.org/debian unstable/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get: 452 http://deb.debian.org/debian unstable/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB] Get: 453 http://deb.debian.org/debian unstable/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get: 454 http://deb.debian.org/debian unstable/main amd64 r-cran-bh all 1.84.0-1 [5912 B] Get: 455 http://deb.debian.org/debian unstable/main amd64 r-cran-cpp11 all 0.5.0-1 [213 kB] Get: 456 http://deb.debian.org/debian unstable/main amd64 r-bioc-biocparallel amd64 1.38.0-2 [1325 kB] Get: 457 http://deb.debian.org/debian unstable/main amd64 r-bioc-iranges amd64 2.38.1-1 [2305 kB] Get: 458 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 459 http://deb.debian.org/debian unstable/main amd64 r-bioc-zlibbioc all 1.50.0+dfsg-2 [9876 B] Get: 460 http://deb.debian.org/debian unstable/main amd64 r-bioc-xvector amd64 0.44.0-1 [622 kB] Get: 461 http://deb.debian.org/debian unstable/main amd64 r-cran-curl amd64 5.2.3+dfsg-1 [178 kB] Get: 462 http://deb.debian.org/debian unstable/main amd64 r-cran-jsonlite amd64 1.8.9+dfsg-1 [445 kB] Get: 463 http://deb.debian.org/debian unstable/main amd64 r-cran-mime amd64 0.12-2 [35.6 kB] Get: 464 http://deb.debian.org/debian unstable/main amd64 r-cran-sys amd64 3.4.3-1 [44.4 kB] Get: 465 http://deb.debian.org/debian unstable/main amd64 r-cran-askpass amd64 1.2.1-1 [24.2 kB] Get: 466 http://deb.debian.org/debian unstable/main amd64 r-cran-openssl amd64 2.2.0+dfsg-1 [401 kB] Get: 467 http://deb.debian.org/debian unstable/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get: 468 http://deb.debian.org/debian unstable/main amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] Get: 469 http://deb.debian.org/debian unstable/main amd64 r-bioc-ucsc.utils all 1.0.0+ds-2 [77.0 kB] Get: 470 http://deb.debian.org/debian unstable/main amd64 r-bioc-genomeinfodbdata all 1.2.12-1 [12.6 MB] Get: 471 http://deb.debian.org/debian unstable/main amd64 r-bioc-genomeinfodb all 1.40.1+dfsg-1 [3843 kB] Get: 472 http://deb.debian.org/debian unstable/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get: 473 http://deb.debian.org/debian unstable/main amd64 r-bioc-biostrings amd64 2.72.1+dfsg-1 [13.3 MB] Get: 474 http://deb.debian.org/debian unstable/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get: 475 http://deb.debian.org/debian unstable/main amd64 r-cran-matrix amd64 1.7-1-1 [4138 kB] Get: 476 http://deb.debian.org/debian unstable/main amd64 r-cran-matrixstats amd64 1.4.1-1 [510 kB] Get: 477 http://deb.debian.org/debian unstable/main amd64 r-bioc-matrixgenerics all 1.16.0-2 [423 kB] Get: 478 http://deb.debian.org/debian unstable/main amd64 r-cran-abind all 1.4-8-1 [68.1 kB] Get: 479 http://deb.debian.org/debian unstable/main amd64 r-bioc-s4arrays amd64 1.4.1+dfsg-1 [524 kB] Get: 480 http://deb.debian.org/debian unstable/main amd64 r-bioc-sparsearray amd64 1.4.8+dfsg-1 [1254 kB] Get: 481 http://deb.debian.org/debian unstable/main amd64 r-bioc-delayedarray amd64 0.30.1+dfsg-1 [1847 kB] Get: 482 http://deb.debian.org/debian unstable/main amd64 r-bioc-genomicranges amd64 1.56.2+dfsg-1 [1843 kB] Get: 483 http://deb.debian.org/debian unstable/main amd64 r-bioc-summarizedexperiment all 1.34.0+dfsg-1 [1102 kB] Get: 484 http://deb.debian.org/debian unstable/main amd64 r-cran-locfit amd64 1.5-9.10-1 [515 kB] Get: 485 http://deb.debian.org/debian unstable/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get: 486 http://deb.debian.org/debian unstable/main amd64 r-cran-glue amd64 1.8.0-1 [165 kB] Get: 487 http://deb.debian.org/debian unstable/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB] Get: 488 http://deb.debian.org/debian unstable/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get: 489 http://deb.debian.org/debian unstable/main amd64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get: 490 http://deb.debian.org/debian unstable/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get: 491 http://deb.debian.org/debian unstable/main amd64 r-cran-mass amd64 7.3-61-1 [1112 kB] Get: 492 http://deb.debian.org/debian unstable/main amd64 r-cran-nlme amd64 3.1.166-1 [2330 kB] Get: 493 http://deb.debian.org/debian unstable/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get: 494 http://deb.debian.org/debian unstable/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB] Get: 495 http://deb.debian.org/debian unstable/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get: 496 http://deb.debian.org/debian unstable/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB] Get: 497 http://deb.debian.org/debian unstable/main amd64 r-cran-munsell all 0.5.1-1 [237 kB] Get: 498 http://deb.debian.org/debian unstable/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get: 499 http://deb.debian.org/debian unstable/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get: 500 http://deb.debian.org/debian unstable/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get: 501 http://deb.debian.org/debian unstable/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get: 502 http://deb.debian.org/debian unstable/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get: 503 http://deb.debian.org/debian unstable/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get: 504 http://deb.debian.org/debian unstable/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get: 505 http://deb.debian.org/debian unstable/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get: 506 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 507 http://deb.debian.org/debian unstable/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get: 508 http://deb.debian.org/debian unstable/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get: 509 http://deb.debian.org/debian unstable/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get: 510 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get: 511 http://deb.debian.org/debian unstable/main amd64 r-cran-rcpp amd64 1.0.13-1-1 [2074 kB] Get: 512 http://deb.debian.org/debian unstable/main amd64 r-cran-rcpparmadillo amd64 14.2.2-1-1 [864 kB] Get: 513 http://deb.debian.org/debian unstable/main amd64 r-bioc-deseq2 amd64 1.44.0+dfsg-1 [1283 kB] Get: 514 http://deb.debian.org/debian unstable/main amd64 r-cran-bitops amd64 1.0-8-1 [30.7 kB] Get: 515 http://deb.debian.org/debian unstable/main amd64 r-bioc-rhtslib amd64 3.0.0+dfsg-1 [1334 kB] Get: 516 http://deb.debian.org/debian unstable/main amd64 r-bioc-rsamtools amd64 2.20.0+dfsg-1 [3600 kB] Get: 517 http://deb.debian.org/debian unstable/main amd64 r-bioc-genomicalignments amd64 1.40.0-1 [2160 kB] Get: 518 http://deb.debian.org/debian unstable/main amd64 r-cran-xml amd64 3.99-0.17-1 [1761 kB] Get: 519 http://deb.debian.org/debian unstable/main amd64 r-cran-rcurl amd64 1.98-1.16+dfsg-1 [799 kB] Get: 520 http://deb.debian.org/debian unstable/main amd64 r-cran-rjson amd64 0.2.23-1 [100.0 kB] Get: 521 http://deb.debian.org/debian unstable/main amd64 r-cran-yaml amd64 2.3.10-1 [108 kB] Get: 522 http://deb.debian.org/debian unstable/main amd64 r-cran-restfulr amd64 0.0.15-1 [382 kB] Get: 523 http://deb.debian.org/debian unstable/main amd64 r-bioc-rtracklayer amd64 1.64.0-1 [5061 kB] Get: 524 http://deb.debian.org/debian unstable/main amd64 r-bioc-tximport all 1.32.0+dfsg-1 [91.2 kB] Get: 525 http://deb.debian.org/debian unstable/main amd64 r-cran-backports amd64 1.5.0-2 [121 kB] Get: 526 http://deb.debian.org/debian unstable/main amd64 r-cran-base64enc amd64 0.1-3-3 [27.9 kB] Get: 527 http://deb.debian.org/debian unstable/main amd64 r-cran-bit amd64 4.0.5-1 [1070 kB] Get: 528 http://deb.debian.org/debian unstable/main amd64 r-cran-bit64 amd64 4.0.5-1 [463 kB] Get: 529 http://deb.debian.org/debian unstable/main amd64 r-cran-boot all 1.3-31-1 [639 kB] Get: 530 http://deb.debian.org/debian unstable/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB] Get: 531 http://deb.debian.org/debian unstable/main amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [223 kB] Get: 532 http://deb.debian.org/debian unstable/main amd64 r-cran-dplyr amd64 1.1.4-4 [1543 kB] Get: 533 http://deb.debian.org/debian unstable/main amd64 r-cran-purrr amd64 1.0.2-1 [507 kB] Get: 534 http://deb.debian.org/debian unstable/main amd64 r-cran-stringi amd64 1.8.4-1 [895 kB] Get: 535 http://deb.debian.org/debian unstable/main amd64 r-cran-stringr all 1.5.1-1 [296 kB] Get: 536 http://deb.debian.org/debian unstable/main amd64 r-cran-tidyr amd64 1.3.1-1 [1163 kB] Get: 537 http://deb.debian.org/debian unstable/main amd64 r-cran-broom all 1.0.7+dfsg-1 [1846 kB] Get: 538 http://deb.debian.org/debian unstable/main amd64 r-cran-fastmap amd64 1.2.0-1 [72.2 kB] Get: 539 http://deb.debian.org/debian unstable/main amd64 r-cran-cachem amd64 1.1.0-1 [73.9 kB] Get: 540 http://deb.debian.org/debian unstable/main amd64 r-cran-digest amd64 0.6.37-1 [206 kB] Get: 541 http://deb.debian.org/debian unstable/main amd64 r-cran-htmltools amd64 0.5.8.1-1 [378 kB] Get: 542 http://deb.debian.org/debian unstable/main amd64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.1 kB] Get: 543 http://deb.debian.org/debian unstable/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB] Get: 544 http://deb.debian.org/debian unstable/main amd64 r-cran-fs amd64 1.6.4+dfsg-1 [247 kB] Get: 545 http://deb.debian.org/debian unstable/main amd64 r-cran-rappdirs amd64 0.3.3-1 [47.4 kB] Get: 546 http://deb.debian.org/debian unstable/main amd64 r-cran-sass amd64 0.4.9+dfsg-1 [965 kB] Get: 547 http://deb.debian.org/debian unstable/main amd64 r-cran-bslib all 0.7.0+dfsg-1 [4365 kB] Get: 548 http://deb.debian.org/debian unstable/main amd64 r-cran-cardata all 3.0.5-1 [1797 kB] Get: 549 http://deb.debian.org/debian unstable/main amd64 r-cran-formula all 1.2-5-1 [158 kB] Get: 550 http://deb.debian.org/debian unstable/main amd64 r-cran-nnet amd64 7.3-19-2 [111 kB] Get: 551 http://deb.debian.org/debian unstable/main amd64 r-cran-minqa amd64 1.2.8-1 [118 kB] Get: 552 http://deb.debian.org/debian unstable/main amd64 r-cran-nloptr amd64 2.1.1-1 [256 kB] Get: 553 http://deb.debian.org/debian unstable/main amd64 r-cran-rcppeigen amd64 0.3.4.0.2-1 [1411 kB] Get: 554 http://deb.debian.org/debian unstable/main amd64 r-cran-statmod amd64 1.5.0-1 [295 kB] Get: 555 http://deb.debian.org/debian unstable/main amd64 r-cran-lme4 amd64 1.1-35.5-1 [4126 kB] Get: 556 http://deb.debian.org/debian unstable/main amd64 r-cran-numderiv all 2016.8-1.1-3 [115 kB] Get: 557 http://deb.debian.org/debian unstable/main amd64 r-cran-cowplot all 1.1.3+dfsg-1 [638 kB] Get: 558 http://deb.debian.org/debian unstable/main amd64 r-cran-deriv all 4.1.6-1 [151 kB] Get: 559 http://deb.debian.org/debian unstable/main amd64 r-cran-modelr all 0.1.11-1 [204 kB] Get: 560 http://deb.debian.org/debian unstable/main amd64 r-cran-microbenchmark amd64 1.5.0-1 [67.1 kB] Get: 561 http://deb.debian.org/debian unstable/main amd64 r-cran-doby all 4.6.24-1 [4777 kB] Get: 562 http://deb.debian.org/debian unstable/main amd64 r-cran-evaluate all 1.0.0-1 [112 kB] Get: 563 http://deb.debian.org/debian unstable/main amd64 r-cran-xfun amd64 0.49+dfsg-1 [546 kB] Get: 564 http://deb.debian.org/debian unstable/main amd64 r-cran-highr all 0.11+dfsg-1 [38.3 kB] Get: 565 http://deb.debian.org/debian unstable/main amd64 r-cran-knitr all 1.49+dfsg-1 [861 kB] Get: 566 http://deb.debian.org/debian unstable/main amd64 r-cran-pbkrtest all 0.5.3-1 [180 kB] Get: 567 http://deb.debian.org/debian unstable/main amd64 r-cran-sparsem amd64 1.84-2-1+b1 [794 kB] Get: 568 http://deb.debian.org/debian unstable/main amd64 r-cran-matrixmodels all 0.5-3-1 [364 kB] Get: 569 http://deb.debian.org/debian unstable/main amd64 r-cran-survival amd64 3.7-0-1 [6305 kB] Get: 570 http://deb.debian.org/debian unstable/main amd64 r-cran-class amd64 7.3-22-2 [87.3 kB] Get: 571 http://deb.debian.org/debian unstable/main amd64 r-cran-proxy amd64 0.4-27-1 [182 kB] Get: 572 http://deb.debian.org/debian unstable/main amd64 r-cran-e1071 amd64 1.7-16-1 [562 kB] Get: 573 http://deb.debian.org/debian unstable/main amd64 r-cran-iterators all 1.0.14-1 [337 kB] Get: 574 http://deb.debian.org/debian unstable/main amd64 r-cran-foreach all 1.5.2-1 [122 kB] Get: 575 http://deb.debian.org/debian unstable/main amd64 r-cran-data.table amd64 1.16.2+dfsg-1 [1978 kB] Get: 576 http://deb.debian.org/debian unstable/main amd64 r-cran-modelmetrics amd64 1.2.2.2-1+b1 [125 kB] Get: 577 http://deb.debian.org/debian unstable/main amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] Get: 578 http://deb.debian.org/debian unstable/main amd64 r-cran-proc amd64 1.18.5-1 [987 kB] Get: 579 http://deb.debian.org/debian unstable/main amd64 r-cran-tzdb amd64 0.4.0-2 [499 kB] Get: 580 http://deb.debian.org/debian unstable/main amd64 r-cran-clock amd64 0.7.1-1 [1784 kB] Get: 581 http://deb.debian.org/debian unstable/main amd64 r-cran-gower amd64 1.0.1-1 [207 kB] Get: 582 http://deb.debian.org/debian unstable/main amd64 r-cran-hardhat all 1.4.0+dfsg-1 [668 kB] Get: 583 http://deb.debian.org/debian unstable/main amd64 r-cran-rpart amd64 4.1.23-1 [685 kB] Get: 584 http://deb.debian.org/debian unstable/main amd64 r-cran-shape all 1.4.6.1-1 [752 kB] Get: 585 http://deb.debian.org/debian unstable/main amd64 r-cran-diagram all 1.6.5-2 [656 kB] Get: 586 http://deb.debian.org/debian unstable/main amd64 r-cran-kernsmooth amd64 2.23-24-1 [92.7 kB] Get: 587 http://deb.debian.org/debian unstable/main amd64 r-cran-globals all 0.16.3-1 [120 kB] Get: 588 http://deb.debian.org/debian unstable/main amd64 r-cran-listenv all 0.9.1+dfsg-1 [112 kB] Get: 589 http://deb.debian.org/debian unstable/main amd64 r-cran-parallelly amd64 1.38.0-1 [388 kB] Get: 590 http://deb.debian.org/debian unstable/main amd64 r-cran-future all 1.34.0+dfsg-1 [649 kB] Get: 591 http://deb.debian.org/debian unstable/main amd64 r-cran-future.apply all 1.11.2+dfsg-1 [172 kB] Get: 592 http://deb.debian.org/debian unstable/main amd64 r-cran-progressr all 0.14.0-1 [337 kB] Get: 593 http://deb.debian.org/debian unstable/main amd64 r-cran-squarem all 2021.1-1 [179 kB] Get: 594 http://deb.debian.org/debian unstable/main amd64 r-cran-lava all 1.7.3+dfsg-1 [2207 kB] Get: 595 http://deb.debian.org/debian unstable/main amd64 r-cran-prodlim amd64 2024.06.25-1 [416 kB] Get: 596 http://deb.debian.org/debian unstable/main amd64 r-cran-ipred amd64 0.9-15-1 [387 kB] Get: 597 http://deb.debian.org/debian unstable/main amd64 r-cran-timechange amd64 0.3.0-1 [173 kB] Get: 598 http://deb.debian.org/debian unstable/main amd64 r-cran-lubridate amd64 1.9.3+dfsg-1 [1018 kB] Get: 599 http://deb.debian.org/debian unstable/main amd64 r-cran-timedate amd64 4041.110-1 [1211 kB] Get: 600 http://deb.debian.org/debian unstable/main amd64 r-cran-recipes all 1.1.0+dfsg-1 [2047 kB] Get: 601 http://deb.debian.org/debian unstable/main amd64 r-cran-reshape2 amd64 1.4.4-2 [114 kB] Get: 602 http://deb.debian.org/debian unstable/main amd64 r-cran-caret amd64 6.0-94+dfsg-1 [3446 kB] Get: 603 http://deb.debian.org/debian unstable/main amd64 r-cran-conquer amd64 1.3.3-1 [471 kB] Get: 604 http://deb.debian.org/debian unstable/main amd64 r-cran-quantreg amd64 5.99.1-1 [1441 kB] Get: 605 http://deb.debian.org/debian unstable/main amd64 r-cran-foreign amd64 0.8.87-1 [253 kB] Get: 606 http://deb.debian.org/debian unstable/main amd64 r-cran-ellipsis amd64 0.3.2-2 [35.1 kB] Get: 607 http://deb.debian.org/debian unstable/main amd64 r-cran-forcats all 1.0.0-1 [413 kB] Get: 608 http://deb.debian.org/debian unstable/main amd64 r-cran-hms all 1.1.3-1 [104 kB] Get: 609 http://deb.debian.org/debian unstable/main amd64 r-cran-clipr all 0.8.0-1 [53.0 kB] Get: 610 http://deb.debian.org/debian unstable/main amd64 r-cran-prettyunits all 1.2.0-1 [162 kB] Get: 611 http://deb.debian.org/debian unstable/main amd64 r-cran-progress all 1.2.3-1 [93.0 kB] Get: 612 http://deb.debian.org/debian unstable/main amd64 r-cran-vroom amd64 1.6.5-1 [830 kB] Get: 613 http://deb.debian.org/debian unstable/main amd64 r-cran-readr amd64 2.1.5-1 [759 kB] Get: 614 http://deb.debian.org/debian unstable/main amd64 r-cran-haven amd64 2.5.4-1 [342 kB] Get: 615 http://deb.debian.org/debian unstable/main amd64 r-cran-rematch all 2.0.0-1 [18.2 kB] Get: 616 http://deb.debian.org/debian unstable/main amd64 r-cran-cellranger all 1.1.0-3 [100 kB] Get: 617 http://deb.debian.org/debian unstable/main amd64 r-cran-readxl amd64 1.4.3-1 [723 kB] Get: 618 http://deb.debian.org/debian unstable/main amd64 r-cran-writexl amd64 1.5.1-1 [147 kB] Get: 619 http://deb.debian.org/debian unstable/main amd64 r-cran-r.methodss3 all 1.8.2-1 [84.5 kB] Get: 620 http://deb.debian.org/debian unstable/main amd64 r-cran-r.oo all 1.26.0-1 [961 kB] Get: 621 http://deb.debian.org/debian unstable/main amd64 r-cran-r.utils all 2.12.3-1 [1396 kB] Get: 622 http://deb.debian.org/debian unstable/main amd64 r-cran-zip amd64 2.3.1-1 [118 kB] Get: 623 http://deb.debian.org/debian unstable/main amd64 r-cran-openxlsx amd64 4.2.7.1-1 [2014 kB] Get: 624 http://deb.debian.org/debian unstable/main amd64 r-cran-rio all 1.2.3-1 [531 kB] Get: 625 http://deb.debian.org/debian unstable/main amd64 r-cran-car all 3.1-3-1 [1533 kB] Get: 626 http://deb.debian.org/debian unstable/main amd64 r-cran-fontawesome all 0.5.2-1 [1286 kB] Get: 627 http://deb.debian.org/debian unstable/main amd64 r-cran-tinytex all 0.53-1 [146 kB] Get: 628 http://deb.debian.org/debian unstable/main amd64 r-cran-later amd64 1.3.2+dfsg-1 [118 kB] Get: 629 http://deb.debian.org/debian unstable/main amd64 r-cran-promises amd64 1.3.0+dfsg-1 [284 kB] Get: 630 http://deb.debian.org/debian unstable/main amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [493 kB] Get: 631 http://deb.debian.org/debian unstable/main amd64 r-cran-xtable all 1:1.8-4-2 [689 kB] Get: 632 http://deb.debian.org/debian unstable/main amd64 r-cran-sourcetools amd64 0.1.7-1-1 [45.9 kB] Get: 633 http://deb.debian.org/debian unstable/main amd64 r-cran-commonmark amd64 1.9.2-2 [122 kB] Get: 634 http://deb.debian.org/debian unstable/main amd64 r-cran-shiny all 1.9.1+dfsg-1 [3126 kB] Get: 635 http://deb.debian.org/debian unstable/main amd64 r-cran-rmarkdown all 2.28+dfsg-1 [1474 kB] Get: 636 http://deb.debian.org/debian unstable/main amd64 r-cran-htmlwidgets all 1.6.4+dfsg-1 [123 kB] Get: 637 http://deb.debian.org/debian unstable/main amd64 r-cran-miniui all 0.1.1.1-3 [35.9 kB] Get: 638 http://deb.debian.org/debian unstable/main amd64 r-cran-shinyjs all 2.1.0-1 [1009 kB] Get: 639 http://deb.debian.org/debian unstable/main amd64 r-cran-colourpicker all 1.3.0+dfsg-1 [1212 kB] Get: 640 http://deb.debian.org/debian unstable/main amd64 r-cran-corrplot all 0.94-1 [134 kB] Get: 641 http://deb.debian.org/debian unstable/main amd64 r-cran-lazyeval amd64 0.2.2-1+b1 [142 kB] Get: 642 http://deb.debian.org/debian unstable/main amd64 r-cran-crosstalk all 1.2.1+dfsg-1 [175 kB] Get: 643 http://deb.debian.org/debian unstable/main amd64 r-cran-dt all 0.33+dfsg-1 [248 kB] Get: 644 http://deb.debian.org/debian unstable/main amd64 r-cran-ggrepel amd64 0.9.5-2 [251 kB] Get: 645 http://deb.debian.org/debian unstable/main amd64 r-cran-ggsci all 3.2.0-1 [2103 kB] Get: 646 http://deb.debian.org/debian unstable/main amd64 r-cran-ggsignif all 0.6.4-1 [589 kB] Get: 647 http://deb.debian.org/debian unstable/main amd64 r-cran-gridextra all 2.3-3 [1024 kB] Get: 648 http://deb.debian.org/debian unstable/main amd64 r-cran-polynom all 1.4-1+dfsg-1 [92.5 kB] Get: 649 http://deb.debian.org/debian unstable/main amd64 r-cran-rstatix all 0.7.2-1 [609 kB] Get: 650 http://deb.debian.org/debian unstable/main amd64 r-cran-ggpubr all 0.6.0-1 [2080 kB] Get: 651 http://deb.debian.org/debian unstable/main amd64 r-cran-plotly all 4.10.4+dfsg-2 [3634 kB] Get: 652 http://deb.debian.org/debian unstable/main amd64 r-cran-gprofiler2 all 0.2.3+dfsg-1 [121 kB] Get: 653 http://deb.debian.org/debian unstable/main amd64 r-cran-pheatmap all 1.0.12-2 [77.9 kB] Get: 654 http://deb.debian.org/debian unstable/main amd64 salmon amd64 1.10.2+ds1-1+b4 [3404 kB] Get: 655 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB] Get: 656 http://deb.debian.org/debian unstable/main amd64 snakemake all 7.32.4-6 [318 kB] Get: 657 http://deb.debian.org/debian unstable/main amd64 trim-galore all 0.6.10-1 [17.8 MB] Fetched 582 MB in 9s (63.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:amd64. (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 ... 19966 files and directories currently installed.) Preparing to unpack .../libapparmor1_3.1.7-1+b3_amd64.deb ... Unpacking libapparmor1:amd64 (3.1.7-1+b3) ... Selecting previously unselected package libsystemd-shared:amd64. Preparing to unpack .../libsystemd-shared_257-2_amd64.deb ... Unpacking libsystemd-shared:amd64 (257-2) ... Selecting previously unselected package systemd. Preparing to unpack .../systemd_257-2_amd64.deb ... Unpacking systemd (257-2) ... Setting up libapparmor1:amd64 (3.1.7-1+b3) ... Setting up libsystemd-shared:amd64 (257-2) ... Setting up systemd (257-2) ... Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' -> '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' -> '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' -> '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. Selecting previously unselected package systemd-sysv. (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 ... 20922 files and directories currently installed.) Preparing to unpack .../00-systemd-sysv_257-2_amd64.deb ... Unpacking systemd-sysv (257-2) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../01-libdbus-1-3_1.16.0-1_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.16.0-1) ... Selecting previously unselected package dbus-bin. Preparing to unpack .../02-dbus-bin_1.16.0-1_amd64.deb ... Unpacking dbus-bin (1.16.0-1) ... Selecting previously unselected package dbus-session-bus-common. Preparing to unpack .../03-dbus-session-bus-common_1.16.0-1_all.deb ... Unpacking dbus-session-bus-common (1.16.0-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../04-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package dbus-daemon. Preparing to unpack .../05-dbus-daemon_1.16.0-1_amd64.deb ... Unpacking dbus-daemon (1.16.0-1) ... Selecting previously unselected package dbus-system-bus-common. Preparing to unpack .../06-dbus-system-bus-common_1.16.0-1_all.deb ... Unpacking dbus-system-bus-common (1.16.0-1) ... Selecting previously unselected package dbus. Preparing to unpack .../07-dbus_1.16.0-1_amd64.deb ... Unpacking dbus (1.16.0-1) ... Selecting previously unselected package autoconf-archive. Preparing to unpack .../08-autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package pigz. Preparing to unpack .../09-pigz_2.8-1_amd64.deb ... Unpacking pigz (2.8-1) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../10-libpython3.12-minimal_3.12.8-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.8-3) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../11-python3.12-minimal_3.12.8-3_amd64.deb ... Unpacking python3.12-minimal (3.12.8-3) ... Setting up libpython3.12-minimal:amd64 (3.12.8-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22525 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_amd64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.2~rc1-2_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2~rc1-2) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-6_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.8-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.8-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.8-3_amd64.deb ... Unpacking python3.12 (3.12.8-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23588 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_amd64.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../001-libpython3.13-minimal_3.13.1-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.1-2) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../002-python3.13-minimal_3.13.1-2_amd64.deb ... Unpacking python3.13-minimal (3.13.1-2) ... Selecting previously unselected package sgml-base. Preparing to unpack .../003-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../004-libproc2-0_2%3a4.0.4-6_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../005-procps_2%3a4.0.4-6_amd64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../006-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../007-openssl_3.3.2-2_amd64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../008-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../009-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../010-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../011-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../012-gettext-base_0.22.5-3_amd64.deb ... Unpacking gettext-base (0.22.5-3) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../013-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../014-groff-base_1.23.0-6_amd64.deb ... Unpacking groff-base (1.23.0-6) ... Selecting previously unselected package libpam-systemd:amd64. Preparing to unpack .../015-libpam-systemd_257-2_amd64.deb ... Unpacking libpam-systemd:amd64 (257-2) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../016-bsdextrautils_2.40.2-12_amd64.deb ... Unpacking bsdextrautils (2.40.2-12) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../017-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../018-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package ucf. Preparing to unpack .../019-ucf_3.0045_all.deb ... Moving old data out of the way Unpacking ucf (3.0045) ... Selecting previously unselected package libgdk-pixbuf2.0-common. Preparing to unpack .../020-libgdk-pixbuf2.0-common_2.42.12+dfsg-1_all.deb ... Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... 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Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Setting up libllvm19:amd64 (1:19.1.5-1) ... Setting up libx11-xcb1:amd64 (2:1.8.10-2) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up liblapack3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-3) ... Setting up libxdamage1:amd64 (1:1.1.6-1+b2) ... Setting up libatk1.0-0t64:amd64 (2.54.0-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b3) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1+b1) ... Setting up libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-15) ... Setting up libcloudproviders0:amd64 (0.3.6-1+b1) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libnss3:amd64 (2:3.106-1) ... Setting up dbus-daemon (1.16.0-1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up libcolord2:amd64 (1.4.7-1+b2) ... Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b3) ... Setting up libtbbbind-2-5:amd64 (2021.12.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libdconf1:amd64 (0.40.0-4+b3) ... Setting up dh-autoreconf (20) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up coinor-libcoinutils3v5:amd64 (2.11.11+ds-2) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libmbedx509-7:amd64 (3.6.2-3) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up pandoc (3.1.11.1+ds-2) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b3) ... Setting up libjs-jquery-metadata (12-4) ... Setting up dbus (1.16.0-1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b1) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libxrandr2:amd64 (2:1.5.4-1+b2) ... Setting up ucf (3.0045) ... Setting up libjs-sphinxdoc (8.1.3-2) ... Setting up coinor-libosi1v5:amd64 (0.108.10+ds-1+b1) ... Setting up libmbedtls21:amd64 (3.6.2-3) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... Setting up groff-base (1.23.0-6) ... Setting up libwayland-cursor0:amd64 (1.23.0-1+b1) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1.1+b1) ... Setting up libpam-systemd:amd64 (257-2) ... Setting up libharfbuzz0b:amd64 (10.1.0-1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1+b1) ... Setting up libsnappy-java (1.1.10.7-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b2) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libcommons-codec-java (1.17.1-1) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.1-2) ... Setting up libavahi-client3:amd64 (0.8-15) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up libpython3.13:amd64 (3.13.1-2) ... Setting up libpaper1:amd64 (1.1.29+b2) ... Creating config file /etc/papersize with new version Setting up gtk-update-icon-cache (4.16.7+ds-1) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b3) ... Setting up openjdk-21-jre-headless:amd64 (21.0.5+11-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libcurl4t64:amd64 (8.11.1-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up python3.13 (3.13.1-2) ... Setting up libcommons-io-java (2.17.0-1) ... Setting up libdrm-radeon1:amd64 (2.4.123-1) ... Setting up libxtst6:amd64 (2:1.2.3-1.1+b3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.15-1) ... Setting up libxcursor1:amd64 (1:1.2.2-1+b1) ... Setting up libpango-1.0-0:amd64 (1.55.0+ds-3) ... Setting up libdrm-intel1:amd64 (2.4.123-1) ... Setting up python3.12-tk (3.12.8-3) ... Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-2) ... Setting up libcurl3t64-gnutls:amd64 (8.11.1-1) ... Setting up libtbb12:amd64 (2021.12.0-1) ... Setting up libpaper-utils (1.1.29+b2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' -> '/usr/lib/systemd/system/man-db.timer'. Setting up libcairo2:amd64 (1.18.2-2) ... Setting up python3.13-tk (3.13.1-2) ... Setting up dbus-user-session (1.16.0-1) ... Setting up adwaita-icon-theme (47.0-2) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up coinor-libclp1:amd64 (1.17.10+ds-1) ... Setting up libatspi2.0-0t64:amd64 (2.54.0-1) ... Setting up libraqm0:amd64 (0.10.2-1) ... Setting up sphinx-common (8.1.3-2) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b1) ... Setting up git (1:2.45.2-1.2) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up libhts3t64:amd64 (1.20+ds-2) ... Setting up libbigwig0t64:amd64 (0.4.7+dfsg-3.1+b2) ... Setting up libcairo-gobject2:amd64 (1.18.2-2) ... Setting up coinor-libcgl1:amd64 (0.60.9+ds-1) ... Setting up libpangoft2-1.0-0:amd64 (1.55.0+ds-3) ... Setting up libcups2t64:amd64 (2.4.10-2) ... Setting up libpangocairo-1.0-0:amd64 (1.55.0+ds-3) ... Setting up libncbi-ngs3:amd64 (3.0.9+dfsg-7+b1) ... Setting up libatk-bridge2.0-0t64:amd64 (2.54.0-1) ... Setting up mesa-libgallium:amd64 (24.2.8-1) ... Setting up libngs-jni:amd64 (3.0.9+dfsg-7+b1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up libpython3.12-stdlib:amd64 (3.12.8-3) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libgbm1:amd64 (24.2.8-1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3.12 (3.12.8-3) ... Setting up libgl1-mesa-dri:amd64 (24.2.8-1) ... Setting up libstaden-read14t64:amd64 (1.15.0-1.1+b2) ... Setting up debhelper (13.21) ... Setting up dconf-service (0.40.0-4+b3) ... Setting up samtools (1.20-3) ... Setting up libpython3.12t64:amd64 (3.12.8-3) ... Setting up salmon (1.10.2+ds1-1+b4) ... Setting up r-base-core (4.4.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.5.2-1) ... Setting up r-cran-squarem (2021.1-1) ... Setting up megadepth (1.2.0-4+b1) ... Setting up r-cran-labeling (0.4.3-1) ... Setting up coinor-libcbc3.1:amd64 (2.10.12+ds-1) ... Setting up r-cran-sourcetools (0.1.7-1-1) ... Setting up r-cran-futile.options (1.0.1-3) ... Setting up r-cran-lattice (0.22-6-1) ... Setting up r-cran-nlme (3.1.166-1) ... Setting up r-cran-farver (2.1.2-1) ... Setting up r-cran-formatr (1.14-2) ... Setting up r-cran-formula (1.2-5-1) ... Setting up r-cran-zip (2.3.1-1) ... Setting up r-cran-xml (3.99-0.17-1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up r-cran-locfit (1.5-9.10-1) ... Setting up r-cran-sparsem (1.84-2-1+b1) ... Setting up r-cran-statmod (1.5.0-1) ... Setting up r-cran-nnet (7.3-19-2) ... Setting up r-cran-lazyeval (0.2.2-1+b1) ... Setting up r-cran-clipr (0.8.0-1) ... Setting up r-cran-polynom (1.4-1+dfsg-1) ... Setting up r-cran-commonmark (1.9.2-2) ... Setting up r-cran-rjson (0.2.23-1) ... Setting up r-cran-proxy (0.4-27-1) ... Setting up libngs-java:amd64 (3.0.9+dfsg-7+b1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.4-1) ... Setting up r-cran-numderiv (2016.8-1.1-3) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up r-cran-rappdirs (0.3.3-1) ... Setting up libhtsjdk-java (4.1.0+dfsg-2) ... Setting up r-bioc-genomeinfodbdata (1.2.12-1) ... Setting up r-cran-microbenchmark (1.5.0-1) ... Setting up libpython3-stdlib:amd64 (3.12.7-1) ... Setting up r-cran-littler (0.3.20-2) ... Setting up r-cran-bh (1.84.0-1) ... Setting up r-cran-fs (1.6.4+dfsg-1) ... Setting up r-cran-rcpp (1.0.13-1-1) ... Setting up r-cran-curl (5.2.3+dfsg-1) ... Setting up r-cran-codetools (0.2-20-1) ... Setting up r-cran-nloptr (2.1.1-1) ... Setting up r-cran-boot (1.3-31-1) ... Setting up r-cran-rematch (2.0.0-1) ... Setting up r-bioc-biocgenerics (0.50.0-2) ... Setting up r-cran-rlang (1.1.4-1) ... Setting up libglx-mesa0:amd64 (24.2.8-1) ... Setting up r-cran-matrixstats (1.4.1-1) ... Setting up r-cran-listenv (0.9.1+dfsg-1) ... Setting up littler (0.3.20-2) ... Setting up libglx0:amd64 (1.7.0-1+b2) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-4+b3) ... Setting up r-bioc-matrixgenerics (1.16.0-2) ... Setting up r-cran-xfun (0.49+dfsg-1) ... Setting up r-cran-sys (3.4.3-1) ... Setting up r-cran-withr (3.0.2+dfsg-1) ... Setting up r-cran-backports (1.5.0-2) ... Setting up r-cran-deriv (4.1.6-1) ... Setting up r-cran-mime (0.12-2) ... Setting up r-cran-generics (0.1.3-1) ... Setting up r-cran-base64enc (0.1-3-3) ... Setting up r-cran-iterators (1.0.14-1) ... Setting up r-cran-abind (1.4-8-1) ... Setting up r-cran-digest (0.6.37-1) ... Setting up r-cran-yaml (2.3.10-1) ... Setting up r-cran-lambda.r (1.2.4-2) ... Setting up r-cran-gower (1.0.1-1) ... Setting up r-cran-evaluate (1.0.0-1) ... Setting up r-cran-timedate (4041.110-1) ... Setting up r-cran-highr (0.11+dfsg-1) ... Setting up r-cran-foreach (1.5.2-1) ... Setting up r-cran-prettyunits (1.2.0-1) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up r-cran-cardata (3.0.5-1) ... Setting up r-cran-mass (7.3-61-1) ... Setting up python3 (3.12.7-1) ... Setting up r-cran-snow (1:0.4.4-2) ... Setting up python3-zipp (3.21.0-1) ... Setting up r-cran-data.table (1.16.2+dfsg-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up r-cran-glue (1.8.0-1) ... Setting up r-cran-foreign (0.8.87-1) ... Setting up r-cran-writexl (1.5.1-1) ... Setting up r-cran-bit (4.0.5-1) ... Setting up python3-markupsafe (2.1.5-1+b2) ... Setting up r-cran-xtable (1:1.8-4-2) ... Setting up r-cran-cli (3.6.3-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up r-cran-bitops (1.0-8-1) ... Setting up python3-plac (1.4.3-2) ... Setting up python3-platformdirs (4.3.6-1) ... Setting up python3-psutil (5.9.8-2) ... Setting up r-cran-bit64 (4.0.5-1) ... Setting up python3-tz (2024.2-1) ... Setting up r-cran-progressr (0.14.0-1) ... Setting up r-bioc-zlibbioc (1.50.0+dfsg-2) ... Setting up python3-ratelimiter (1.2.0.post0-4) ... Setting up r-cran-shape (1.4.6.1-1) ... Setting up r-cran-askpass (1.2.1-1) ... Setting up r-cran-fastmap (1.2.0-1) ... Setting up r-cran-r.methodss3 (1.8.2-1) ... Setting up r-bioc-biobase (2.64.0-4) ... Setting up r-cran-jsonlite (1.8.9+dfsg-1) ... Setting up python3-pil:amd64 (10.4.0-1+b1) ... Setting up r-cran-corrplot (0.94-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up python3-roman (4.2-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-jinja2 (3.1.3-1.1) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up python3-packaging (24.2-1) ... Setting up r-cran-colorspace (2.1-1+dfsg-1) ... Setting up r-cran-parallelly (1.38.0-1) ... Setting up libgl1:amd64 (1.7.0-1+b2) ... Setting up coinor-cbc (2.10.12+ds-1) ... Setting up r-cran-stringi (1.8.4-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-humanfriendly (10.0-6) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up r-cran-cpp11 (0.5.0-1) ... Setting up r-cran-plyr (1.8.9-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up python3-brotli (1.1.0-2+b6) ... Setting up r-bioc-s4vectors (0.42.1+dfsg-2) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up python3-mdurl (0.1.2-1) ... Setting up r-cran-futile.logger (1.4.3-4) ... Setting up r-cran-diagram (1.6.5-2) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-dpath (2.2.0-1) ... Setting up python3-connection-pool (0.0.3-2) ... Setting up python3-kiwisolver (1.4.7-2+b1) ... Setting up r-cran-gtable (0.3.6+dfsg-1) ... Setting up python3-idna (3.8-2) ... Setting up python3-wrapt (1.15.0-3+b1) ... Setting up python3-markdown (3.7-2) ... Setting up python3-throttler (1.2.2-2) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up r-cran-later (1.3.2+dfsg-1) ... Setting up r-cran-matrix (1.7-1-1) ... Setting up r-cran-htmltools (0.5.8.1-1) ... Setting up r-cran-tinytex (0.53-1) ... Setting up python3-urllib3 (2.2.3-4) ... Setting up r-bioc-tximport (1.32.0+dfsg-1) ... Setting up python3-markdown-it (3.0.0-2) ... Setting up r-cran-kernsmooth (2.23-24-1) ... Setting up r-cran-knitr (1.49+dfsg-1) ... Setting up python3-rpds-py (0.21.0-2) ... Setting up python3-fastjsonschema (2.20.0-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up hisat2 (2.2.1-5) ... Setting up python3-lxml:amd64 (5.3.0-1+b1) ... Setting up python3-traitlets (5.14.3+really5.14.3-1) ... Setting up r-cran-cachem (1.1.0-1) ... Setting up r-cran-sass (0.4.9+dfsg-1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-py2bit (0.3.2-1) ... Setting up r-cran-rcpparmadillo (14.2.2-1-1) ... Setting up r-bioc-iranges (2.38.1-1) ... Setting up python3-datrie:amd64 (0.8.2-5+b1) ... Setting up r-cran-tzdb (0.4.0-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-lzstring (1.0.4-3) ... Setting up r-cran-globals (0.16.3-1) ... Setting up r-cran-rcurl (1.98-1.16+dfsg-1) ... Setting up python3-coloredlogs (15.0.1-1) ... Setting up python3-smmap (6.0.0-1) ... Setting up r-cran-restfulr (0.0.15-1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up python3-jupyter-core (5.7.2-5) ... Setting up libgtk-3-common (3.24.43-4) ... Setting up r-cran-rcppeigen (0.3.4.0.2-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up python3-toposort (1.10-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-configargparse (1.7-2) ... Setting up r-cran-ellipsis (0.3.2-2) ... Setting up python3-sympy (1.13.3-1) ... Setting up r-cran-minqa (1.2.8-1) ... Setting up python3-attr (24.2.0-1) ... Setting up r-cran-openssl (2.2.0+dfsg-1) ... Setting up python3-pysam (0.22.1+ds-2+b2) ... Setting up r-bioc-s4arrays (1.4.1+dfsg-1) ... Setting up r-cran-stringr (1.5.1-1) ... Setting up python3-importlib-metadata (8.5.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up r-cran-class (7.3-22-2) ... Setting up python3-smart-open (7.1.0-1) ... Setting up r-bioc-biocparallel (1.38.0-2) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up r-cran-modelmetrics (1.2.2.2-1+b1) ... Setting up r-cran-openxlsx (4.2.7.1-1) ... Setting up python3-deeptoolsintervals (0.1.9-3+b10) ... Setting up python3-colorama (0.4.6-4) ... Setting up python3-lz4 (4.4.0+dfsg-1) ... Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-pulp (2.7.0+dfsg-4) ... /usr/lib/python3/dist-packages/pulp/apis/xpress_api.py:322: SyntaxWarning: invalid escape sequence '\ ' """ /usr/lib/python3/dist-packages/pulp/apis/xpress_api.py:322: SyntaxWarning: invalid escape sequence '\ ' """ Setting up r-cran-matrixmodels (0.5-3-1) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b3) ... Setting up r-bioc-rhtslib (3.0.0+dfsg-1) ... Setting up python3-tenacity (8.4.2+really8.4.1-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up r-cran-munsell (0.5.1-1) ... Setting up r-cran-tibble (3.2.1+dfsg-2) ... Setting up r-cran-clock (0.7.1-1) ... Setting up r-cran-proc (1.18.5-1) ... Setting up r-cran-fontawesome (0.5.2-1) ... Setting up python3-tabulate (0.9.0-1) ... Setting up python3-all (3.12.7-1) ... Setting up python3-yaml (6.0.2-1+b1) ... Setting up python3-tk:amd64 (3.13.1-1) ... Setting up r-cran-survival (3.7-0-1) ... Setting up r-bioc-biocio (1.14.0+dfsg-1) ... Setting up python3-gitdb (4.0.11-1) ... Setting up r-cran-r.oo (1.26.0-1) ... Setting up python3-click (8.1.7-2) ... Setting up r-cran-future (1.34.0+dfsg-1) ... Setting up r-cran-forcats (1.0.0-1) ... Setting up r-cran-jquerylib (0.1.4+dfsg-4) ... Setting up r-cran-lme4 (1.1-35.5-1) ... Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... Setting up python3-yte (1.5.4-1) ... Setting up r-cran-reshape2 (1.4.4-2) ... Setting up r-cran-future.apply (1.11.2+dfsg-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pyaml-env (1.2.1-2) ... /usr/lib/python3/dist-packages/pyaml_env/parse_config.py:58: SyntaxWarning: invalid escape sequence '\w' type_tag_pattern = re.compile(f'({type_tag}\w+\s)') /usr/lib/python3/dist-packages/pyaml_env/parse_config.py:58: SyntaxWarning: invalid escape sequence '\w' type_tag_pattern = re.compile(f'({type_tag}\w+\s)') Setting up r-cran-timechange (0.3.0-1) ... Setting up python3-pil.imagetk:amd64 (10.4.0-1+b1) ... Setting up r-cran-httr (1.4.7+dfsg-1) ... Setting up python3-git (3.1.37-3) ... Setting up libgtk-3-0t64:amd64 (3.24.43-4) ... Setting up r-cran-gridextra (2.3-3) ... Setting up r-cran-hms (1.1.3-1) ... Setting up r-cran-scales (1.3.0-1) ... Setting up r-cran-memoise (2.0.1-1) ... Setting up r-cran-lava (1.7.3+dfsg-1) ... Setting up r-cran-promises (1.3.0+dfsg-1) ... Setting up r-cran-purrr (1.0.2-1) ... Setting up r-cran-e1071 (1.7-16-1) ... Setting up r-bioc-xvector (0.44.0-1) ... Setting up r-cran-hardhat (1.4.0+dfsg-1) ... Setting up r-cran-dplyr (1.1.4-4) ... Setting up r-cran-progress (1.2.3-1) ... Setting up python3-referencing (0.35.1-2) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up r-cran-pheatmap (1.0.12-2) ... Setting up r-cran-lubridate (1.9.3+dfsg-1) ... Setting up r-cran-r.utils (2.12.3-1) ... Setting up r-cran-vroom (1.6.5-1) ... Setting up r-cran-prodlim (2024.06.25-1) ... Setting up python3-py (1.11.0-2) ... Setting up r-bioc-ucsc.utils (1.0.0+ds-2) ... Setting up python3-babel (2.16.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up r-bioc-sparsearray (1.4.8+dfsg-1) ... Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... Setting up r-cran-ggsignif (0.6.4-1) ... Setting up r-cran-cellranger (1.1.0-3) ... Setting up r-cran-httpuv (1.6.15+dfsg-1) ... Setting up r-cran-rpart (4.1.23-1) ... Setting up r-cran-ggsci (3.2.0-1) ... Setting up python3-networkx (3.2.1-5) ... Setting up r-cran-ipred (0.9-15-1) ... Setting up python3-fs (2.4.16-5.1) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-xopen (1.7.0-2) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up r-bioc-genomeinfodb (1.40.1+dfsg-1) ... Setting up r-cran-bslib (0.7.0+dfsg-1) ... Setting up r-cran-readr (2.1.5-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up r-cran-ggrepel (0.9.5-2) ... Setting up r-cran-tidyr (1.3.1-1) ... Setting up python3-retry (0.9.2-3) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up r-cran-recipes (1.1.0+dfsg-1) ... Setting up python3-colormath (3.0.0-4) ... /usr/lib/python3/dist-packages/colormath/chromatic_adaptation.py:85: SyntaxWarning: invalid escape sequence '\*' logger.debug(" \* Applying adaptation matrix: %s", adaptation) /usr/lib/python3/dist-packages/colormath/color_appearance_models.py:684: SyntaxWarning: invalid escape sequence '\s' """ /usr/lib/python3/dist-packages/colormath/color_appearance_models.py:788: SyntaxWarning: invalid escape sequence '\s' """ /usr/lib/python3/dist-packages/colormath/color_conversions.py:40: SyntaxWarning: invalid escape sequence '\*' logger.debug(" \* Applying RGB conversion matrix: %s->%s", /usr/lib/python3/dist-packages/colormath/color_conversions.py:488: SyntaxWarning: invalid escape sequence '\-' logger.debug(" \- Target RGB space: %s", target_rgb) /usr/lib/python3/dist-packages/colormath/color_conversions.py:490: SyntaxWarning: invalid escape sequence '\-' logger.debug(" \- Target native illuminant: %s", target_illum) /usr/lib/python3/dist-packages/colormath/color_conversions.py:491: SyntaxWarning: invalid escape sequence '\-' logger.debug(" \- XYZ color's illuminant: %s", cobj.illuminant) /usr/lib/python3/dist-packages/colormath/color_conversions.py:497: SyntaxWarning: invalid escape sequence '\*' logger.debug(" \* Applying transformation from %s to %s ", /usr/lib/python3/dist-packages/colormath/color_conversions.py:503: SyntaxWarning: invalid escape sequence '\*' logger.debug(" \* New values: %.3f, %.3f, %.3f", /usr/lib/python3/dist-packages/colormath/color_objects.py:452: SyntaxWarning: invalid escape sequence '\-' logger.debug(" \- Original illuminant: %s", self.illuminant) /usr/lib/python3/dist-packages/colormath/color_objects.py:453: SyntaxWarning: invalid escape sequence '\-' logger.debug(" \- Target illuminant: %s", target_illuminant) /usr/lib/python3/dist-packages/colormath/color_objects.py:459: SyntaxWarning: invalid escape sequence '\*' logger.debug(" \* Applying transformation from %s to %s ", /usr/lib/python3/dist-packages/colormath/chromatic_adaptation.py:85: SyntaxWarning: invalid escape sequence '\*' logger.debug(" \* Applying adaptation matrix: %s", adaptation) /usr/lib/python3/dist-packages/colormath/color_appearance_models.py:684: SyntaxWarning: invalid escape sequence '\s' """ /usr/lib/python3/dist-packages/colormath/color_appearance_models.py:788: SyntaxWarning: invalid escape sequence '\s' """ /usr/lib/python3/dist-packages/colormath/color_conversions.py:40: SyntaxWarning: invalid escape sequence '\*' logger.debug(" \* Applying RGB conversion matrix: %s->%s", /usr/lib/python3/dist-packages/colormath/color_conversions.py:488: SyntaxWarning: invalid escape sequence '\-' logger.debug(" \- Target RGB space: %s", target_rgb) /usr/lib/python3/dist-packages/colormath/color_conversions.py:490: SyntaxWarning: invalid escape sequence '\-' logger.debug(" \- Target native illuminant: %s", target_illum) /usr/lib/python3/dist-packages/colormath/color_conversions.py:491: SyntaxWarning: invalid escape sequence '\-' logger.debug(" \- XYZ color's illuminant: %s", cobj.illuminant) /usr/lib/python3/dist-packages/colormath/color_conversions.py:497: SyntaxWarning: invalid escape sequence '\*' logger.debug(" \* Applying transformation from %s to %s ", /usr/lib/python3/dist-packages/colormath/color_conversions.py:503: SyntaxWarning: invalid escape sequence '\*' logger.debug(" \* New values: %.3f, %.3f, %.3f", /usr/lib/python3/dist-packages/colormath/color_objects.py:452: SyntaxWarning: invalid escape sequence '\-' logger.debug(" \- Original illuminant: %s", self.illuminant) /usr/lib/python3/dist-packages/colormath/color_objects.py:453: SyntaxWarning: invalid escape sequence '\-' logger.debug(" \- Target illuminant: %s", target_illuminant) /usr/lib/python3/dist-packages/colormath/color_objects.py:459: SyntaxWarning: invalid escape sequence '\*' logger.debug(" \* Applying transformation from %s to %s ", Setting up python3-pybigwig (0.3.23+dfsg-1+b1) ... Setting up python3-stopit (1.1.2-3) ... Setting up python3-contourpy (1.3.1-1) ... Setting up python3-humanize (4.11.0-1) ... Setting up python3-jsonschema-specifications (2023.12.1-2) ... Setting up python3-htseq (2.0.9+dfsg-1) ... Setting up r-bioc-delayedarray (0.30.1+dfsg-1) ... Setting up python3-dnaio (1.2.3-1) ... Setting up r-cran-cowplot (1.1.3+dfsg-1) ... Setting up r-cran-readxl (1.4.3-1) ... Setting up python3-scipy (1.14.1-3) ... Setting up python3-spectra (0.0.11-4) ... Setting up python3-rich (13.7.1-1) ... Setting up r-cran-haven (2.5.4-1) ... Setting up r-bioc-genomicranges (1.56.2+dfsg-1) ... Setting up r-bioc-biostrings (2.72.1+dfsg-1) ... Setting up r-cran-caret (6.0-94+dfsg-1) ... Setting up r-cran-shiny (1.9.1+dfsg-1) ... Setting up r-cran-shinyjs (2.1.0-1) ... Setting up r-cran-miniui (0.1.1.1-3) ... Setting up python3-cutadapt (4.7-2+b2) ... Setting up r-cran-broom (1.0.7+dfsg-1) ... Setting up python3-jsonschema (4.19.2-5) ... Setting up r-cran-rmarkdown (2.28+dfsg-1) ... Setting up r-cran-conquer (1.3.3-1) ... Setting up r-bioc-rsamtools (2.20.0+dfsg-1) ... Setting up python3-rich-click (1.6.0-1) ... Setting up r-cran-crosstalk (1.2.1+dfsg-1) ... Setting up r-cran-rio (1.2.3-1) ... Setting up r-bioc-summarizedexperiment (1.34.0+dfsg-1) ... Setting up r-cran-quantreg (5.99.1-1) ... Setting up cutadapt (4.7-2) ... Setting up r-bioc-deseq2 (1.44.0+dfsg-1) ... Setting up python3-nbformat (5.9.1-1) ... Setting up r-cran-modelr (0.1.11-1) ... Setting up r-cran-htmlwidgets (1.6.4+dfsg-1) ... Setting up r-cran-colourpicker (1.3.0+dfsg-1) ... Setting up python3-plotly (5.20.0+dfsg-1) ... Setting up r-cran-doby (4.6.24-1) ... Setting up r-bioc-genomicalignments (1.40.0-1) ... Setting up r-bioc-rtracklayer (1.64.0-1) ... Setting up r-cran-dt (0.33+dfsg-1) ... Setting up trim-galore (0.6.10-1) ... Setting up r-cran-plotly (4.10.4+dfsg-2) ... Setting up r-cran-pbkrtest (0.5.3-1) ... Setting up r-cran-car (3.1-3-1) ... Setting up r-cran-gprofiler2 (0.2.3+dfsg-1) ... Setting up r-cran-rstatix (0.7.2-1) ... Setting up r-cran-ggpubr (0.6.0-1) ... Setting up python3-fonttools (4.55.0-3) ... Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... Setting up python3-matplotlib (3.8.3-3+b1) ... Setting up multiqc (1.21+dfsg-2) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for systemd (257-2) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up openjdk-21-jre:amd64 (21.0.5+11-1) ... Setting up default-jre-headless (2:1.21-76) ... Setting up default-jre (2:1.21-76) ... Setting up fastqc (0.12.1+dfsg-4) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up snakemake (7.32.4-6) ... Setting up python3-sphinx (8.1.3-2) ... Setting up python3-numpydoc (1.8.0-1) ... Setting up python3-deeptools (3.5.5+dfsg-1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/pigx-rnaseq-0.1.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pigx-rnaseq_0.1.1-1_source.changes dpkg-buildpackage: info: source package pigx-rnaseq dpkg-buildpackage: info: source version 0.1.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.1.1' dh_auto_clean rm -rf pigx-common rm -f config.log test.sh rm -rf tests/output rm -f Makefile.in aclocal.m4 build-aux/install-sh build-aux/missing build-aux/test-driver rm -f scripts/jquery.min.js rm -f conftest.tar confdefs.h make[1]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.1.1' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/pigx-rnaseq.substvars debian/files rm -fr -- debian/pigx-rnaseq/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config debian/rules execute_before_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.1.1' mkdir -p /build/reproducible-path/pigx-rnaseq-0.1.1/pigx-common cp -a debian/common /build/reproducible-path/pigx-rnaseq-0.1.1/pigx-common make[1]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.1.1' dh_autoreconf find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i aclocal: warning: couldn't open directory 'm4': No such file or directory configure.ac:6: installing 'build-aux/install-sh' configure.ac:6: installing 'build-aux/missing' parallel-tests: installing 'build-aux/test-driver' find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.1.1' dh_auto_configure -- GUNZIP=/bin/gunzip SED=/bin/sed ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking GUNZIP=/bin/gunzip SED=/bin/sed checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking how to create a pax tar archive... gnutar checking whether make supports nested variables... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for a Python interpreter with version >= 3.5... python3 checking for python3... /usr/bin/python3 checking for python3 version... 3.12 checking for python3 platform... linux checking for GNU default python3 prefix... ${prefix} checking for GNU default python3 exec_prefix... ${exec_prefix} checking for python3 script directory (pythondir)... ${PYTHON_PREFIX}/lib/python3.12/site-packages checking for python3 extension module directory (pyexecdir)... ${PYTHON_EXEC_PREFIX}/lib/python3.12/site-packages checking python3 module: yaml... yes configure: Using /bin/gunzip as gunzip executable. configure: Using /bin/sed as sed executable. configure: Using /bin/bash as bash executable. checking for snakemake... /usr/bin/snakemake checking for pandoc... /usr/bin/pandoc configure: Using /usr/bin/STAR as STAR executable. checking for hisat2... /usr/bin/hisat2 checking for hisat2-build... /usr/bin/hisat2-build checking for multiqc... /usr/bin/multiqc checking for fastp... /usr/bin/fastp configure: Using /usr/bin/salmon as salmon executable. checking for R... /usr/bin/R checking for Rscript... /usr/bin/Rscript checking for bamCoverage... /usr/bin/bamCoverage checking for megadepth... /usr/bin/megadepth checking R package rmarkdown ... yes checking R package knitr ... yes checking R package ggplot2 ... yes checking R package ggrepel ... yes checking R package DESeq2 ... yes checking R package DT ... yes checking R package pheatmap ... yes checking R package corrplot ... yes checking R package reshape2 ... yes checking R package plotly ... yes checking R package scales ... yes checking R package crosstalk ... yes checking R package gprofiler2 ... yes checking R package ggpubr ... yes checking R package rtracklayer ... yes checking R package SummarizedExperiment ... yes checking R package tximport ... yes checking R package rjson ... yes checking for samtools... /usr/bin/samtools configure: Environment variables will be captured. checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating META config.status: creating etc/settings.yaml config.status: creating scripts/deseqReport.Rmd config.status: creating Makefile config.status: creating qsub-template.sh config.status: creating test.sh config.status: creating tests/test_hisat2/test.sh config.status: creating tests/test_salmon/test_salmon_index.sh config.status: creating tests/test_salmon/test_salmon_quant.sh config.status: creating tests/test_salmon_counts/test.sh config.status: creating tests/test_hisat2_counts/test.sh config.status: creating tests/test_multiqc/test.sh config.status: creating tests/test_deseq_reports/test.sh config.status: creating tests/test_genome_coverage/test.sh config.status: creating pigx-rnaseq make[1]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.1.1' dh_auto_build make -j42 make[1]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.1.1' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.1.1' rm -f debian/pigx-rnaseq.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.1.1' ln -sf /usr/share/javascript/jquery/jquery.min.js scripts/ #/usr/bin/make -j2 check VERBOSE=1 ./test.sh Commencing snakemake run submission locally Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 6 Rules claiming more threads will be scaled down. Job stats: job count --------------------------------- ------- all 1 check_annotation_files 1 collate_read_counts 1 count_reads 6 counts_from_SALMON 1 coverage_megadepth 6 hisat2_index 1 hisat2_map 6 index_bam 6 multiqc 1 norm_counts_deseq 1 record_annotation_files 1 report1 1 report2 1 report3 1 salmon_index 1 salmon_quant 6 translate_sample_sheet_for_report 1 trim_qc_reads_pe 4 trim_qc_reads_se 2 total 49 Select jobs to execute... [Mon Jan 19 20:29:59 2026] rule trim_qc_reads_se: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/HBR_Rep1.read1.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep1.se.fastp.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep1.se.fastp.json log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.HBR_Rep1.log jobid: 5 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/HBR_Rep1.read1.fastq.gz --out1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz -h /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep1.se.fastp.html -j /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep1.se.fastp.json >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.HBR_Rep1.log 2>&1 [Mon Jan 19 20:29:59 2026] rule trim_qc_reads_pe: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep2.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep2.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep2.pe.fastp.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep2.pe.fastp.json log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.UHR_Rep2.log jobid: 13 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep2.read1.fastq.gz --in2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep2.read2.fastq.gz --out1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz --out2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz -h /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep2.pe.fastp.html -j /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep2.pe.fastp.json >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.UHR_Rep2.log 2>&1 [Mon Jan 19 20:29:59 2026] rule translate_sample_sheet_for_report: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_sheet.csv output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv jobid: 24 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv resources: tmpdir=/tmp /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//translate_sample_sheet_for_report.R /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_sheet.csv [Mon Jan 19 20:29:59 2026] rule trim_qc_reads_pe: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep1.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep1.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep1.pe.fastp.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep1.pe.fastp.json log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.UHR_Rep1.log jobid: 11 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep1.read1.fastq.gz --in2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep1.read2.fastq.gz --out1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz --out2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz -h /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep1.pe.fastp.html -j /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep1.pe.fastp.json >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.UHR_Rep1.log 2>&1 [Mon Jan 19 20:29:59 2026] rule trim_qc_reads_se: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep3.read1.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep3.se.fastp.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep3.se.fastp.json log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.UHR_Rep3.log jobid: 15 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep3.read1.fastq.gz --out1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz -h /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep3.se.fastp.html -j /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep3.se.fastp.json >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.UHR_Rep3.log 2>&1 [Mon Jan 19 20:29:59 2026] rule trim_qc_reads_pe: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/HBR_Rep3.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/HBR_Rep3.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep3.pe.fastp.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep3.pe.fastp.json log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.HBR_Rep3.log jobid: 9 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/HBR_Rep3.read1.fastq.gz --in2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/HBR_Rep3.read2.fastq.gz --out1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz --out2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz -h /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep3.pe.fastp.html -j /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep3.pe.fastp.json >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.HBR_Rep3.log 2>&1 [Mon Jan 19 20:29:59 2026] Finished job 24. 1 of 49 steps (2%) done Select jobs to execute... [Mon Jan 19 20:29:59 2026] rule check_annotation_files: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.fasta, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.cdna.fasta, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/input_annotation_stats.tsv log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/check_annotation_files.log jobid: 1 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/input_annotation_stats.tsv resources: tmpdir=/tmp /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//validate_input_annotation.R /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.cdna.fasta /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.fasta /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/check_annotation_files.log 2>&1 [Mon Jan 19 20:29:59 2026] Finished job 5. 2 of 49 steps (4%) done Select jobs to execute... [Mon Jan 19 20:29:59 2026] rule trim_qc_reads_pe: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/HBR_Rep2.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep2.pe.fastp.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep2.pe.fastp.json log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.HBR_Rep2.log jobid: 7 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/HBR_Rep2.read1.fastq.gz --in2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz --out1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz --out2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz -h /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep2.pe.fastp.html -j /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep2.pe.fastp.json >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.HBR_Rep2.log 2>&1 [Mon Jan 19 20:29:59 2026] Finished job 15. 3 of 49 steps (6%) done Select jobs to execute... [Mon Jan 19 20:29:59 2026] rule record_annotation_files: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.fasta, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.cdna.fasta, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/annotations.tgz log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/record_annotation_files.log jobid: 48 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/annotations.tgz resources: tmpdir=/tmp mkdir /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/annotations; cp /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.cdna.fasta /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.fasta /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/annotations tar -czvf annotations.tgz /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/annotations --remove-files >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/record_annotation_files.log 2>&1 [Mon Jan 19 20:29:59 2026] Finished job 9. 4 of 49 steps (8%) done [Mon Jan 19 20:29:59 2026] Finished job 11. 5 of 49 steps (10%) done [Mon Jan 19 20:29:59 2026] Finished job 13. 6 of 49 steps (12%) done [Mon Jan 19 20:30:00 2026] Finished job 7. 7 of 49 steps (14%) done [Mon Jan 19 20:30:00 2026] Finished job 48. 8 of 49 steps (16%) done [Mon Jan 19 20:30:09 2026] Finished job 1. 9 of 49 steps (18%) done Select jobs to execute... [Mon Jan 19 20:30:09 2026] rule salmon_index: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.cdna.fasta, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/input_annotation_stats.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_index.log jobid: 4 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/input_annotation_stats.tsv resources: tmpdir=/tmp, mem_mb=5000, mem_mib=4769 /usr/bin/salmon index -t /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.cdna.fasta -i /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index -p 8 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_index.log 2>&1 [Mon Jan 19 20:30:09 2026] rule hisat2_index: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.fasta, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/input_annotation_stats.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2_index.log jobid: 17 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/input_annotation_stats.tsv resources: tmpdir=/tmp, mem_mb=32000, mem_mib=30518 /usr/bin/hisat2-build -f -p 2 --large-index /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.fasta /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2_index.log 2>&1 [Mon Jan 19 20:30:11 2026] Finished job 4. 10 of 49 steps (20%) done Select jobs to execute... [Mon Jan 19 20:30:11 2026] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.genes.sf log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_UHR_Rep1.log jobid: 10 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 [Mon Jan 19 20:30:11 2026] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.genes.sf log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_HBR_Rep3.log jobid: 8 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 [Mon Jan 19 20:30:11 2026] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.genes.sf log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log jobid: 3 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.genes.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 [Mon Jan 19 20:30:11 2026] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.genes.sf log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_HBR_Rep2.log jobid: 6 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 [Mon Jan 19 20:30:11 2026] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.genes.sf log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log jobid: 14 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.genes.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 [Mon Jan 19 20:30:11 2026] Finished job 17. 11 of 49 steps (22%) done Select jobs to execute... [Mon Jan 19 20:30:11 2026] rule hisat2_map: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_UHR_Rep2.log, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep2.log jobid: 21 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 /usr/bin/hisat2 --fast -x /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_UHR_Rep2.log 2>&1 /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep2.log 2>&1 rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam [Mon Jan 19 20:30:11 2026] Finished job 21. 12 of 49 steps (24%) done Select jobs to execute... [Mon Jan 19 20:30:11 2026] rule hisat2_map: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_HBR_Rep1.log, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep1.log jobid: 16 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 /usr/bin/hisat2 --fast -x /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.out.sam -U /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_HBR_Rep1.log 2>&1 /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep1.log 2>&1 rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.out.sam [Mon Jan 19 20:30:11 2026] Finished job 16. 13 of 49 steps (27%) done Select jobs to execute... [Mon Jan 19 20:30:11 2026] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.genes.sf log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_UHR_Rep2.log jobid: 12 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 Building DAG of jobs... Building DAG of jobs... Building DAG of jobs... Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 6 Rules claiming more threads will be scaled down. Provided resources: mem_mb=6000, mem_mib=5723 Select jobs to execute... Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 6 Rules claiming more threads will be scaled down. Provided resources: mem_mb=6000, mem_mib=5723 Select jobs to execute... Using shell: /usr/bin/bash Provided cores: 6 Rules claiming more threads will be scaled down. Provided resources: mem_mb=6000, mem_mib=5723 Select jobs to execute... Using shell: /usr/bin/bash Provided cores: 6 Rules claiming more threads will be scaled down. Provided resources: mem_mb=6000, mem_mib=5723 Select jobs to execute... Using shell: /usr/bin/bash Provided cores: 6 Rules claiming more threads will be scaled down. Provided resources: mem_mb=6000, mem_mib=5723 Select jobs to execute... /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_UHR_Rep1.log 2>&1 /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_HBR_Rep2.log 2>&1 /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_HBR_Rep3.log 2>&1 /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index -l A -p 8 -r /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log 2>&1 /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index -l A -p 8 -r /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log 2>&1 Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 6 Rules claiming more threads will be scaled down. Provided resources: mem_mb=6000, mem_mib=5723 Select jobs to execute... /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_UHR_Rep2.log 2>&1 [Mon Jan 19 20:30:12 2026] Finished job 3. 14 of 49 steps (29%) done Select jobs to execute... [Mon Jan 19 20:30:12 2026] rule hisat2_map: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_UHR_Rep3.log, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep3.log jobid: 22 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 /usr/bin/hisat2 --fast -x /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.out.sam -U /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_UHR_Rep3.log 2>&1 /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep3.log 2>&1 rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.out.sam [Mon Jan 19 20:30:12 2026] Finished job 14. 15 of 49 steps (31%) done Select jobs to execute... [Mon Jan 19 20:30:12 2026] rule hisat2_map: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_HBR_Rep3.log, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep3.log jobid: 19 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 /usr/bin/hisat2 --fast -x /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.out.sam -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_HBR_Rep3.log 2>&1 /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep3.log 2>&1 rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.out.sam [Mon Jan 19 20:30:12 2026] Finished job 6. 16 of 49 steps (33%) done Select jobs to execute... [Mon Jan 19 20:30:12 2026] rule hisat2_map: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_UHR_Rep1.log, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep1.log jobid: 20 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 /usr/bin/hisat2 --fast -x /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.out.sam -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_UHR_Rep1.log 2>&1 /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep1.log 2>&1 rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.out.sam [Mon Jan 19 20:30:12 2026] Finished job 8. 17 of 49 steps (35%) done [Mon Jan 19 20:30:12 2026] Finished job 10. 18 of 49 steps (37%) done Select jobs to execute... [Mon Jan 19 20:30:12 2026] rule hisat2_map: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_HBR_Rep2.log, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep2.log jobid: 18 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 /usr/bin/hisat2 --fast -x /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.out.sam -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_HBR_Rep2.log 2>&1 /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep2.log 2>&1 rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.out.sam [Mon Jan 19 20:30:12 2026] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_HBR_Rep1.log jobid: 27 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_HBR_Rep1.log 2>&1 Select jobs to execute... [Mon Jan 19 20:30:12 2026] Finished job 27. 19 of 49 steps (39%) done [Mon Jan 19 20:30:12 2026] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_UHR_Rep2.log jobid: 35 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_UHR_Rep2.log 2>&1 [Mon Jan 19 20:30:12 2026] Finished job 22. 20 of 49 steps (41%) done Select jobs to execute... [Mon Jan 19 20:30:12 2026] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_UHR_Rep3.log jobid: 37 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_UHR_Rep3.log 2>&1 [Mon Jan 19 20:30:12 2026] Finished job 35. 21 of 49 steps (43%) done Select jobs to execute... [Mon Jan 19 20:30:12 2026] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/UHR_Rep2.count_reads.log jobid: 34 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//count_reads.R UHR_Rep2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/UHR_Rep2.count_reads.log 2>&1 [Mon Jan 19 20:30:12 2026] Finished job 37. 22 of 49 steps (45%) done Select jobs to execute... [Mon Jan 19 20:30:12 2026] rule coverage_megadepth: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep2.log jobid: 43 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep2.log 2>&1 [Mon Jan 19 20:30:12 2026] Finished job 19. 23 of 49 steps (47%) done Select jobs to execute... [Mon Jan 19 20:30:12 2026] rule coverage_megadepth: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log jobid: 44 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log 2>&1 [Mon Jan 19 20:30:12 2026] Finished job 43. 24 of 49 steps (49%) done Select jobs to execute... [Mon Jan 19 20:30:12 2026] rule coverage_megadepth: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log jobid: 39 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log 2>&1 [Mon Jan 19 20:30:12 2026] Finished job 18. 25 of 49 steps (51%) done Select jobs to execute... [Mon Jan 19 20:30:12 2026] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_HBR_Rep2.log jobid: 29 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_HBR_Rep2.log 2>&1 [Mon Jan 19 20:30:12 2026] Finished job 20. 26 of 49 steps (53%) done [Mon Jan 19 20:30:12 2026] Finished job 44. 27 of 49 steps (55%) done Select jobs to execute... [Mon Jan 19 20:30:12 2026] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_HBR_Rep3.log jobid: 31 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_HBR_Rep3.log 2>&1 [Mon Jan 19 20:30:12 2026] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_UHR_Rep1.log jobid: 33 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_UHR_Rep1.log 2>&1 [Mon Jan 19 20:30:12 2026] Finished job 39. 28 of 49 steps (57%) done Select jobs to execute... [Mon Jan 19 20:30:12 2026] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/HBR_Rep1.count_reads.log jobid: 26 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//count_reads.R HBR_Rep1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/HBR_Rep1.count_reads.log 2>&1 [Mon Jan 19 20:30:12 2026] Finished job 31. 29 of 49 steps (59%) done Select jobs to execute... [Mon Jan 19 20:30:12 2026] rule coverage_megadepth: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep3.log jobid: 41 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep3.log 2>&1 Select jobs to execute... [Mon Jan 19 20:30:12 2026] Finished job 29. 30 of 49 steps (61%) done [Mon Jan 19 20:30:12 2026] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/HBR_Rep3.count_reads.log jobid: 30 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//count_reads.R HBR_Rep3 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/HBR_Rep3.count_reads.log 2>&1 [Mon Jan 19 20:30:12 2026] Finished job 33. 31 of 49 steps (63%) done Select jobs to execute... [Mon Jan 19 20:30:12 2026] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/UHR_Rep3.count_reads.log jobid: 36 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//count_reads.R UHR_Rep3 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/UHR_Rep3.count_reads.log 2>&1 [Mon Jan 19 20:30:12 2026] Finished job 41. 32 of 49 steps (65%) done Select jobs to execute... [Mon Jan 19 20:30:12 2026] rule coverage_megadepth: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep2.log jobid: 40 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep2.log 2>&1 [Mon Jan 19 20:30:12 2026] Finished job 12. 33 of 49 steps (67%) done Select jobs to execute... [Mon Jan 19 20:30:12 2026] rule counts_from_SALMON: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_import_counts.log jobid: 23 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.sf resources: tmpdir=/tmp, mem_mb=200, mem_mib=191 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//counts_matrix_from_SALMON.R /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_import_counts.log 2>&1 [Mon Jan 19 20:30:12 2026] Finished job 40. 34 of 49 steps (69%) done Select jobs to execute... [Mon Jan 19 20:30:12 2026] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/HBR_Rep2.count_reads.log jobid: 28 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//count_reads.R HBR_Rep2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/HBR_Rep2.count_reads.log 2>&1 [Mon Jan 19 20:30:23 2026] Finished job 23. 35 of 49 steps (71%) done Select jobs to execute... [Mon Jan 19 20:30:23 2026] rule multiqc: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/multiqc/multiqc_report.html log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/multiqc.hisat2.log jobid: 2 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/multiqc/multiqc_report.html; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/multiqc -f -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/multiqc /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/multiqc.hisat2.log 2>&1 [Mon Jan 19 20:30:26 2026] Finished job 36. 36 of 49 steps (73%) done Select jobs to execute... [Mon Jan 19 20:30:26 2026] rule report2: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/analysis1.report.salmon.transcripts.log jobid: 46 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv wildcards: analysis=analysis1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts/runDeseqReport.R --logo=/build/reproducible-path/pigx-rnaseq-0.1.1/images/Logo_PiGx.png --prefix='analysis1.salmon.transcripts' --reportFile=/build/reproducible-path/pigx-rnaseq-0.1.1/scripts/deseqReport.Rmd --countDataFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv --colDataFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv --gtfFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/analysis1.report.salmon.transcripts.log 2>&1 [Mon Jan 19 20:30:26 2026] Finished job 28. 37 of 49 steps (76%) done Select jobs to execute... [Mon Jan 19 20:30:26 2026] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/UHR_Rep1.count_reads.log jobid: 32 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//count_reads.R UHR_Rep1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/UHR_Rep1.count_reads.log 2>&1 [Mon Jan 19 20:30:27 2026] Finished job 2. 38 of 49 steps (78%) done Select jobs to execute... [Mon Jan 19 20:30:27 2026] rule coverage_megadepth: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep1.log jobid: 42 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep1.log 2>&1 [Mon Jan 19 20:30:27 2026] Finished job 30. 39 of 49 steps (80%) done Select jobs to execute... [Mon Jan 19 20:30:27 2026] rule report3: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/analysis1.report.salmon.genes.log jobid: 47 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv wildcards: analysis=analysis1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts/runDeseqReport.R --logo=/build/reproducible-path/pigx-rnaseq-0.1.1/images/Logo_PiGx.png --prefix='analysis1.salmon.genes' --reportFile=/build/reproducible-path/pigx-rnaseq-0.1.1/scripts/deseqReport.Rmd --countDataFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv --colDataFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv --gtfFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/analysis1.report.salmon.genes.log 2>&1 [Mon Jan 19 20:30:27 2026] Finished job 42. 40 of 49 steps (82%) done [Mon Jan 19 20:30:27 2026] Finished job 26. 41 of 49 steps (84%) done [Mon Jan 19 20:30:27 2026] Finished job 34. 42 of 49 steps (86%) done [Mon Jan 19 20:30:41 2026] Finished job 32. 43 of 49 steps (88%) done Select jobs to execute... [Mon Jan 19 20:30:41 2026] rule collate_read_counts: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/collate_read_counts.log jobid: 25 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv resources: tmpdir=/tmp, mem_mb=200, mem_mib=191 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts/collate_read_counts.R /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/collate_read_counts.log 2>&1 [Mon Jan 19 20:30:41 2026] Finished job 25. 44 of 49 steps (90%) done Select jobs to execute... [Mon Jan 19 20:30:41 2026] rule norm_counts_deseq: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/norm_counts_deseq.log jobid: 38 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv resources: tmpdir=/tmp, mem_mb=1000, mem_mib=954 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts/norm_counts_deseq.R /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/norm_counts_deseq.log 2>&1 [Mon Jan 19 20:30:41 2026] rule report1: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/hisat2/analysis1.deseq.report.html log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/analysis1.report.log jobid: 45 reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/hisat2/analysis1.deseq.report.html; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv wildcards: analysis=analysis1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts/runDeseqReport.R --logo=/build/reproducible-path/pigx-rnaseq-0.1.1/images/Logo_PiGx.png --prefix='analysis1' --reportFile=/build/reproducible-path/pigx-rnaseq-0.1.1/scripts/deseqReport.Rmd --countDataFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv --colDataFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv --gtfFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/hisat2 --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/analysis1.report.log 2>&1 [Mon Jan 19 20:30:50 2026] Finished job 38. 45 of 49 steps (92%) done [Mon Jan 19 20:30:50 2026] Finished job 46. 46 of 49 steps (94%) done [Mon Jan 19 20:30:50 2026] Finished job 47. 47 of 49 steps (96%) done [Mon Jan 19 20:31:04 2026] Finished job 45. 48 of 49 steps (98%) done Select jobs to execute... [Mon Jan 19 20:31:04 2026] localrule all: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/input_annotation_stats.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/multiqc/multiqc_report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/hisat2/analysis1.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/annotations.tgz jobid: 0 reason: Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/annotations.tgz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/hisat2/analysis1.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/input_annotation_stats.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/multiqc/multiqc_report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv resources: tmpdir=/tmp [Mon Jan 19 20:31:04 2026] Finished job 0. 49 of 49 steps (100%) done Complete log: .snakemake/log/2026-01-19T202958.762870.snakemake.log The following files have been generated: - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/input_annotation_stats.tsv - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/multiqc/multiqc_report.html - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/hisat2/analysis1.deseq.report.html - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/annotations.tgz make[1]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.1.1' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/pigx-rnaseq.substvars rm -fr -- debian/.debhelper/generated/pigx-rnaseq/ debian/pigx-rnaseq/ debian/tmp/ dh_auto_install --destdir=debian/pigx-rnaseq/ install -m0755 -d /build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq make -j42 install DESTDIR=/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.1.1' make[2]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.1.1' /usr/bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' /usr/bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' /usr/bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq/usr/bin' /usr/bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' /usr/bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq/usr/share/pigx_rnaseq' /usr/bin/install -c snakefile.py qsub-template.sh '/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' /usr/bin/install -c pigx-rnaseq '/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq/usr/bin' /usr/bin/install -c scripts/runDeseqReport.R scripts/translate_sample_sheet_for_report.R scripts/deseqReport.Rmd scripts/counts_matrix_from_SALMON.R scripts/validate_input.py scripts/norm_counts_deseq.R scripts/count_reads.R scripts/collate_read_counts.R scripts/validate_input_annotation.R '/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' /usr/bin/install -c -m 644 README.md '/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' /usr/bin/install -c -m 644 etc/sample_sheet.csv.example etc/settings.yaml etc/pretty.txt images/Logo_PiGx.png '/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq/usr/share/pigx_rnaseq' make[2]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.1.1' make[1]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.1.1' dh_installdocs install -m0755 -d debian/pigx-rnaseq/usr/share/doc/pigx-rnaseq install -m0755 -d debian/pigx-rnaseq/usr/share/doc/pigx-rnaseq cp --reflink=auto -a ./README.md debian/pigx-rnaseq/usr/share/doc/pigx-rnaseq cp --reflink=auto -a ./CONTRIBUTING debian/pigx-rnaseq/usr/share/doc/pigx-rnaseq chmod -R u\+rw,go=rX debian/pigx-rnaseq/usr/share/doc install -p -m0644 debian/copyright debian/pigx-rnaseq/usr/share/doc/pigx-rnaseq/copyright dh_installchangelogs install -m0755 -d debian/pigx-rnaseq/usr/share/doc/pigx-rnaseq install -p -m0644 debian/.debhelper/generated/pigx-rnaseq/dh_installchangelogs.dch.trimmed debian/pigx-rnaseq/usr/share/doc/pigx-rnaseq/changelog.Debian dh_installman install -m0755 -d debian/pigx-rnaseq/usr/share/man/man1/ install -p -m0644 ./debian/pigx-rnaseq.1 debian/pigx-rnaseq/usr/share/man/man1/pigx-rnaseq.1 man-recode --to-code UTF-8 --suffix .dh-new debian/pigx-rnaseq/usr/share/man/man1/pigx-rnaseq.1 mv debian/pigx-rnaseq/usr/share/man/man1/pigx-rnaseq.1.dh-new debian/pigx-rnaseq/usr/share/man/man1/pigx-rnaseq.1 chmod 0644 -- debian/pigx-rnaseq/usr/share/man/man1/pigx-rnaseq.1 dh_perl dh_link dh_strip_nondeterminism Using 1725709225 as canonical time Normalizing debian/pigx-rnaseq/usr/share/pigx_rnaseq/Logo_PiGx.png using File::StripNondeterminism::handlers::png dh_compress cd debian/pigx-rnaseq chmod a-x usr/share/doc/pigx-rnaseq/changelog.Debian usr/share/man/man1/pigx-rnaseq.1 gzip -9nf usr/share/doc/pigx-rnaseq/changelog.Debian usr/share/man/man1/pigx-rnaseq.1 cd '/build/reproducible-path/pigx-rnaseq-0.1.1' debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.1.1' dh_fixperms find debian/pigx-rnaseq ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/pigx-rnaseq/usr/share/doc -type f -a -true -a ! -regex 'debian/pigx-rnaseq/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/pigx-rnaseq/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/pigx-rnaseq/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/pigx-rnaseq -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/pigx-rnaseq/usr/bin debian/pigx-rnaseq/usr/libexec -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/pigx-rnaseq/usr/libexec/pigx_rnaseq -name "*.R" | xargs -r chmod -x find debian/pigx-rnaseq/usr/libexec/pigx_rnaseq -name "*.Rmd" | xargs -r chmod -x find debian/pigx-rnaseq/usr/libexec/pigx_rnaseq -name "*.py" | xargs -r chmod -x make[1]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.1.1' dh_missing dh_installdeb install -m0755 -d debian/pigx-rnaseq/DEBIAN dh_gencontrol install -m0755 -d debian/pigx-rnaseq/DEBIAN echo misc:Depends= >> debian/pigx-rnaseq.substvars echo misc:Pre-Depends= >> debian/pigx-rnaseq.substvars dpkg-gencontrol -ppigx-rnaseq -ldebian/changelog -Tdebian/pigx-rnaseq.substvars -cdebian/control -Pdebian/pigx-rnaseq chmod 0644 -- debian/pigx-rnaseq/DEBIAN/control dh_md5sums install -m0755 -d debian/pigx-rnaseq/DEBIAN cd debian/pigx-rnaseq >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/pigx-rnaseq/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/pigx-rnaseq .. dpkg-deb: building package 'pigx-rnaseq' in '../pigx-rnaseq_0.1.1-1_all.deb'. dpkg-genbuildinfo --build=binary -O../pigx-rnaseq_0.1.1-1_amd64.buildinfo dpkg-genchanges --build=binary -O../pigx-rnaseq_0.1.1-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: 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/1812173 and its subdirectories I: Current time: Mon Jan 19 20:31:13 -12 2026 I: pbuilder-time-stamp: 1768897873 Wed Dec 18 02:08:16 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Wed Dec 18 02:08:16 UTC 2024 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Wed Dec 18 02:21:59 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Wed Dec 18 02:22:00 UTC 2024 I: pigx-rnaseq_0.1.1-1_amd64.changes: Format: 1.8 Date: Sat, 07 Sep 2024 13:40:25 +0200 Source: pigx-rnaseq Binary: pigx-rnaseq Architecture: all Version: 0.1.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: pigx-rnaseq - pipeline for checkpointed and distributed RNA-seq analyses Changes: pigx-rnaseq (0.1.1-1) unstable; urgency=medium . * Team upload. . [Andreas Tille] * Standards-Version: 4.6.2 (routine-update) * Build Salsa CI using python3-htseq from experimental . [Steffen Moeller] * Fixed lintian warnings - Improved d/pigx-rnaseq.1 whatis line - Completed path to m4 file . [ Michael R. Crusoe ] * New upstream version. * Remove constraints unnecessary since bullseye (oldstable): + Build-Depends: Drop versioned constraint on r-cran-dt (>= 0.15+dfsg-2) . + pigx-rnaseq: Drop versioned constraint on r-cran-dt (>= 0.15+dfsg-2) in Depends. * d/copyright: no longer need to exclude the m4 directory (it isn't shipped by upstream anymore) * d/upstream/metadata: fix repo URL, add issue tracker Checksums-Sha1: 225ef6ebd9805ad1ebd8cba9b0abd38399142129 61696 pigx-rnaseq_0.1.1-1_all.deb 0d9a154067f29ba28e9aba6954a4f54b527d5511 25036 pigx-rnaseq_0.1.1-1_amd64.buildinfo Checksums-Sha256: 286ce30816f15c9348617ee7aa74d60a29c39d94b0942b330eee7df942b6192a 61696 pigx-rnaseq_0.1.1-1_all.deb 8939bc756a12a6b55a06af1ba164b0f4c859be34fec07520cf696fdce6078025 25036 pigx-rnaseq_0.1.1-1_amd64.buildinfo Files: 31284ff2cec66262fab4b45074a1c1ad 61696 science optional pigx-rnaseq_0.1.1-1_all.deb b30b4ec605f0bf111076d69799d27d23 25036 science optional pigx-rnaseq_0.1.1-1_amd64.buildinfo Wed Dec 18 02:22:01 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_14-26747.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.tTRzH070/pigx-rnaseq_0.1.1-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.tTRzH070/pigx-rnaseq_0.1.1-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.tTRzH070/pigx-rnaseq_0.1.1-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.tTRzH070/b1/pigx-rnaseq_0.1.1-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.tTRzH070/b2/pigx-rnaseq_0.1.1-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.372s) 0.372s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.021s) 0.021s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 736ms CPU time consumed: 733ms Wed Dec 18 02:22:02 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Wed Dec 18 02:22:02 UTC 2024 I: pigx-rnaseq from unstable built successfully and reproducibly on amd64. Wed Dec 18 02:22:03 UTC 2024 I: Submitting .buildinfo files to external archives: Wed Dec 18 02:22:03 UTC 2024 I: Submitting 28K b1/pigx-rnaseq_0.1.1-1_amd64.buildinfo.asc Wed Dec 18 02:22:04 UTC 2024 I: Submitting 28K b2/pigx-rnaseq_0.1.1-1_amd64.buildinfo.asc Wed Dec 18 02:22:05 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Dec 18 02:22:05 UTC 2024 I: Done submitting .buildinfo files. Wed Dec 18 02:22:05 UTC 2024 I: Removing signed pigx-rnaseq_0.1.1-1_amd64.buildinfo.asc files: removed './b1/pigx-rnaseq_0.1.1-1_amd64.buildinfo.asc' removed './b2/pigx-rnaseq_0.1.1-1_amd64.buildinfo.asc'