Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/pigx-rnaseq/pigx-rnaseq_0.0.10+ds-2_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/pigx-rnaseq-0.0.10+ds-2388w1zvp/pigx-rnaseq_0.0.10+ds-2_all.buildinfo Get source package info: pigx-rnaseq=0.0.10+ds-2 Source URL: http://snapshot.notset.fr/mr/package/pigx-rnaseq/0.0.10+ds-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=ant=1.10.9-1 ant-optional=1.10.9-1 autoconf=2.69-11.1 automake=1:1.16.2-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1~rc1-2 binutils=2.35.1-2 binutils-common=2.35.1-2 binutils-x86-64-linux-gnu=2.35.1-2 bsdextrautils=2.36-3+b1 bsdutils=1:2.36-3+b1 build-essential=12.8 bzip2=1.0.8-4 ca-certificates=20200601 ca-certificates-java=20190909 coinor-cbc=2.10.5+ds1-3 coinor-libcbc3=2.10.5+ds1-3 coinor-libcgl1=0.60.3+repack1-2 coinor-libclp1=1.17.5+repack1-1 coinor-libcoinutils3v5=2.11.4+repack1-1 coinor-libosi1v5=0.108.6+repack1-1 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-15 cutadapt=2.10-1 dash=0.5.10.2-7 debconf=1.5.74 debhelper=13.2.1 debianutils=4.11.2 default-jre=2:1.11-72 default-jre-headless=2:1.11-72 dh-autoreconf=19 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 docutils-common=0.16+dfsg-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 fastqc=0.11.9+dfsg-4 file=1:5.38-5 findutils=4.7.0-1 fontconfig=2.13.1-4.2 fontconfig-config=2.13.1-4.2 fonts-font-awesome=5.0.10+really4.7.0~dfsg-2 fonts-glyphicons-halflings=1.009~3.4.1+dfsg-1 fonts-lato=2.0-2 fonts-lyx=2.3.5.2-1 fonts-mathjax=2.7.9+dfsg-1 g++=4:10.2.0-1 g++-10=10.2.0-15 gcc=4:10.2.0-1 gcc-10=10.2.0-15 gcc-10-base=10.2.0-15 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 git=1:2.28.0-1 git-man=1:2.28.0-1 grep=3.4-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.58 intltool-debian=0.35.0+20060710.5 java-common=0.72 libacl1=2.2.53-8 libactivation-java=1.2.0-2 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node-find-up=4.1.0-2 node-fs.realpath=1.0.0-1 node-function-bind=1.1.1+repack-1 node-get-caller-file=1.0.2-1 node-get-stream=4.1.0-1 node-glob=7.1.6-1 node-glob-parent=5.1.1+~5.1.0-1 node-graceful-fs=4.2.4-1 node-graphlibrary=2.2.0+really2.1.8+dfsg-1 node-growl=1.10.5-2 node-has-flag=4.0.0-1 node-he=1.2.0-1 node-highlight.js=9.12.0+dfsg1-5 node-html5shiv=3.7.3+dfsg-3 node-iconv=2.3.5-4 node-inflight=1.0.6-1 node-inherits=2.0.4-1 node-invert-kv=3.0.1-1 node-is-binary-path=2.1.0-1 node-is-buffer=1.1.6-1 node-is-extglob=2.1.1-1 node-is-glob=4.0.1-1 node-is-number=7.0.0-1 node-is-stream=2.0.0-1 node-isexe=2.0.0-4 node-jquery=3.5.1+dfsg-4 node-js-yaml=3.14.0+dfsg-1 node-kind-of=6.0.3+dfsg-1 node-lcid=1.0.0-1 node-locate-path=5.0.0-2 node-lodash=4.17.20+dfsg-1 node-lodash-packages=4.17.20+dfsg-1 node-lru-cache=5.1.1-5 node-mem=1.1.0-1 node-mimic-fn=3.0.0-1 node-minimatch=3.0.4-4 node-mkdirp=0.5.1-2 node-ms=2.1.2+~cs0.7.31-1 node-normalize-path=3.0.0-2 node-normalize.css=8.0.1-3 node-npm-run-path=2.0.2-2 node-once=1.4.0-3 node-os-locale=4.0.0-1 node-p-finally=1.0.0-2 node-p-limit=2.2.2-1 node-p-locate=2.0.0-1 node-path-dirname=1.0.2-1 node-path-exists=4.0.0-2 node-path-is-absolute=2.0.0-1 node-pump=3.0.0-4 node-readdirp=3.3.0-2 node-repeat-string=1.6.1-1 node-require-directory=2.1.1-1 node-require-main-filename=2.0.0-1 node-rw=1.3.3-2 node-set-blocking=2.0.0-1 node-set-immediate-shim=2.0.0-1 node-shebang-command=1.2.0-1 node-shebang-regex=3.0.0-1 node-signal-exit=3.0.3-1 node-sprintf-js=1.1.2+ds1-1 node-string-width=4.2.0-1 node-strip-ansi=6.0.0-2 node-strip-eof=1.0.0-2 node-strip-json-comments=3.1.1-1 node-supports-color=6.1.0-2 node-to-regex-range=5.0.1-2 node-util=0.10.3-3 node-wcwidth.js=1.0.0-1 node-which=2.0.2-2 node-which-module=2.0.0-1 node-wide-align=1.1.3-1 node-wrap-ansi=4.0.0-2 node-wrappy=1.0.2-1 node-y18n=4.0.0-2 node-yallist=4.0.0-1 node-yargs=15.3.1-1 node-yargs-parser=18.1.3-1 nodejs=12.19.0~dfsg-1 openjdk-11-jre=11.0.9+11-1 openjdk-11-jre-headless=11.0.9+11-1 openssl=1.1.1h-1 pandoc=2.9.2.1-1+b1 pandoc-citeproc=0.17.0.1-1+b1 pandoc-data=2.9.2.1-1 patch=2.7.6-6 perl=5.30.3-4 perl-base=5.30.3-4 perl-modules-5.30=5.30.3-4 pigz=2.4-1+b1 po-debconf=1.0.21 python-babel-localedata=2.8.0+dfsg.1-4 python-matplotlib-data=3.3.2-2 python3=3.8.6-1 python3-alabaster=0.7.8-1.1 python3-all=3.8.6-1 python3-appdirs=1.4.4-1 python3-attr=19.3.0-5 python3-babel=2.8.0+dfsg.1-4 python3-certifi=2020.6.20-1 python3-chardet=3.0.4-7 python3-click=7.1.2-1 python3-colorama=0.4.3-1 python3-coloredlogs=7.3-2 python3-colormath=3.0.0-1 python3-configargparse=0.13.0-2 python3-cutadapt=2.10-1+b1 python3-cycler=0.10.0-3 python3-dateutil=2.8.1-4 python3-datrie=0.8-1+b2 python3-decorator=4.4.2-2 python3-deeptools=3.5.0-1 python3-deeptoolsintervals=0.1.9-3+b1 python3-distutils=3.8.6-1 python3-dnaio=0.4.2-1+b1 python3-docutils=0.16+dfsg-3 python3-future=0.18.2-4 python3-git=3.1.9-1 python3-gitdb=4.0.5-1 python3-htseq=0.12.4-1 python3-humanfriendly=8.2-3 python3-idna=2.10-1 python3-imagesize=1.2.0-2 python3-importlib-metadata=1.6.0-2 python3-ipython-genutils=0.2.0-4 python3-jinja2=2.11.2-1 python3-jsonschema=3.2.0-3 python3-jupyter-core=4.6.3-4 python3-kiwisolver=1.2.0-1+b1 python3-lib2to3=3.8.6-1 python3-lzstring=1.0.4-1 python3-markdown=3.3.2-1 python3-markupsafe=1.1.1-1+b2 python3-matplotlib=3.3.2-2 python3-minimal=3.8.6-1 python3-more-itertools=4.2.0-3 python3-nbformat=5.0.8-1 python3-networkx=2.5+ds-2 python3-numpy=1:1.19.2-2+b1 python3-numpydoc=1.1.0-3 python3-packaging=20.4-1 python3-pil=7.2.0-1+b1 python3-pkg-resources=50.3.0-1 python3-plotly=4.9.0+dfsg-1 python3-psutil=5.7.2-1+b1 python3-pulp=1.6.0+dfsg1-5 python3-py2bit=0.3.0-6 python3-pybigwig=0.3.17-1+b3 python3-pygments=2.7.1+dfsg-1 python3-pyparsing=2.4.7-1 python3-pyrsistent=0.15.5-1+b2 python3-pysam=0.15.4+ds-3+b1 python3-ratelimiter=1.2.0.post0-1 python3-requests=2.24.0+dfsg-1 python3-retrying=1.3.3-4 python3-roman=2.0.0-5 python3-scipy=1.5.2-2+b1 python3-setuptools=50.3.0-1 python3-simplejson=3.17.0-1+b1 python3-six=1.15.0-1 python3-smmap=3.0.4-1 python3-snowballstemmer=2.0.0-2 python3-spectra=0.0.11-2 python3-sphinx=3.2.1-2 python3-toposort=1.5-3 python3-traitlets=5.0.5-1 python3-tz=2020.1-2 python3-urllib3=1.25.9-1 python3-wrapt=1.12.1-4 python3-xopen=0.9.0-1 python3-yaml=5.3.1-3 python3-zipp=1.0.0-3 python3.8=3.8.6-1 python3.8-minimal=3.8.6-1 python3.9=3.9.0-5 python3.9-minimal=3.9.0-5 r-base-core=4.0.3-1 r-bioc-annotate=1.66.0+dfsg-1 r-bioc-annotationdbi=1.50.3-1 r-bioc-biobase=2.48.0-1 r-bioc-biocgenerics=0.34.0-1 r-bioc-biocparallel=1.22.0-2 r-bioc-biostrings=2.56.0-1+b1 r-bioc-delayedarray=0.14.1+dfsg-1 r-bioc-deseq2=1.28.1+dfsg-1 r-bioc-genefilter=1.70.0-1 r-bioc-geneplotter=1.66.0-1 r-bioc-genomeinfodb=1.24.2-1 r-bioc-genomeinfodbdata=1.2.3-1 r-bioc-genomicalignments=1.24.0-1 r-bioc-genomicranges=1.40.0+dfsg-1 r-bioc-iranges=2.22.2-1 r-bioc-rhtslib=1.20.0+dfsg-1 r-bioc-rsamtools=2.4.0-1 r-bioc-rtracklayer=1.48.0-1 r-bioc-s4vectors=0.26.1-1 r-bioc-summarizedexperiment=1.18.2+dfsg-1 r-bioc-tximport=1.16.1+dfsg-1 r-bioc-xvector=0.28.0-1 r-bioc-zlibbioc=1.34.0+dfsg-1 r-cran-askpass=1.1-2 r-cran-assertthat=0.2.1-2 r-cran-backports=1.1.10-1 r-cran-base64enc=0.1-3-3 r-cran-bh=1.66.0-1 r-cran-bit=4.0.4+dfsg-1 r-cran-bit64=4.0.5-1 r-cran-bitops=1.0-6-5 r-cran-blob=1.2.1-2 r-cran-callr=3.5.0-1 r-cran-cli=2.1.0-1 r-cran-colorspace=1.4-1+dfsg-2 r-cran-colourpicker=1.1.0+dfsg-1 r-cran-commonmark=1.7-2 r-cran-corrplot=0.84-3 r-cran-cpp11=0.2.2-1 r-cran-crayon=1.3.4-5 r-cran-crosstalk=1.1.0.1+dfsg-3 r-cran-curl=4.3+dfsg-1+b1 r-cran-data.table=1.13.0+dfsg-1 r-cran-dbi=1.1.0-3 r-cran-desc=1.2.0-3 r-cran-digest=0.6.26-1 r-cran-dplyr=1.0.2-1 r-cran-dt=0.15+dfsg-2 r-cran-ellipsis=0.3.1-1 r-cran-evaluate=0.14-2 r-cran-fansi=0.4.1-1+b1 r-cran-farver=2.0.3-1+b1 r-cran-fastmap=1.0.1-2+b1 r-cran-formatr=1.7-2 r-cran-futile.logger=1.4.3-4 r-cran-futile.options=1.0.1-3 r-cran-generics=0.0.2-3 r-cran-ggplot2=3.3.2+dfsg-2 r-cran-ggrepel=0.8.2-1+b1 r-cran-glue=1.4.2-1 r-cran-gprofiler=0.7.0-2 r-cran-gtable=0.3.0+dfsg-2 r-cran-hexbin=1.28.1-1+b1 r-cran-highr=0.8+dfsg-2 r-cran-htmltools=0.5.0-2 r-cran-htmlwidgets=1.5.2+dfsg-1 r-cran-httpuv=1.5.4+dfsg-1 r-cran-httr=1.4.2-1 r-cran-isoband=0.2.2-1 r-cran-jsonlite=1.7.1+dfsg-1 r-cran-knitr=1.30+dfsg-1 r-cran-labeling=0.3-4 r-cran-lambda.r=1.2.4-2 r-cran-later=1.1.0.1+dfsg-1 r-cran-lattice=0.20-41-1+b1 r-cran-lazyeval=0.2.2-1+b1 r-cran-lifecycle=0.2.0-2 r-cran-littler=0.3.12-1 r-cran-locfit=1.5-9.4-2+b1 r-cran-magrittr=1.5-6 r-cran-markdown=1.1+dfsg-1+b1 r-cran-mass=7.3-53-1 r-cran-matrix=1.2-18-1+b1 r-cran-matrixstats=0.57.0-1 r-cran-memoise=1.1.0-3 r-cran-mgcv=1.8-33-1 r-cran-mime=0.9-1+b1 r-cran-miniui=0.1.1.1-3 r-cran-munsell=0.5.0-2 r-cran-nlme=3.1.149-1 r-cran-openssl=1.4.3+dfsg-1 r-cran-pheatmap=1.0.12-2 r-cran-pillar=1.4.6-1 r-cran-pkgbuild=1.1.0-1 r-cran-pkgconfig=2.0.3-2 r-cran-pkgkitten=0.2.0-1 r-cran-pkgload=1.1.0-1 r-cran-plogr=0.2.0-3 r-cran-plotly=4.9.2.1+dfsg-2 r-cran-plyr=1.8.6-2 r-cran-praise=1.0.0-4 r-cran-prettyunits=1.1.1-2 r-cran-processx=3.4.4-1 r-cran-promises=1.1.1+dfsg-1 r-cran-ps=1.4.0-1 r-cran-purrr=0.3.4-1+b1 r-cran-r6=2.4.1-2 r-cran-rcolorbrewer=1.1-2-3 r-cran-rcpp=1.0.5-1 r-cran-rcpparmadillo=0.10.1.0.0-1 r-cran-rcurl=1.98-1.2-1+b1 r-cran-reshape2=1.4.4-2 r-cran-rjson=0.2.20-2 r-cran-rlang=0.4.8-1 r-cran-rmarkdown=2.4+dfsg-1 r-cran-rprojroot=1.3-2-3 r-cran-rsqlite=2.2.1-1 r-cran-rstudioapi=0.11-2 r-cran-scales=1.1.1-1 r-cran-shiny=1.5.0+dfsg-1 r-cran-shinyjs=2.0.0-1 r-cran-snow=1:0.4.3-2 r-cran-sourcetools=0.1.7-3 r-cran-stringi=1.5.3-1 r-cran-stringr=1.4.0-2 r-cran-survival=3.2-7-1 r-cran-sys=3.4-1 r-cran-testthat=2.3.2-2+b1 r-cran-tibble=3.0.4-1 r-cran-tidyr=1.1.2-1 r-cran-tidyselect=1.1.0+dfsg-1 r-cran-tinytex=0.26-1 r-cran-utf8=1.1.4-2 r-cran-vctrs=0.3.4-1 r-cran-viridislite=0.3.0-4 r-cran-withr=2.3.0-1 r-cran-xfun=0.18-1 r-cran-xml=3.99-0.5-1 r-cran-xtable=1:1.8-4-2 r-cran-yaml=2.2.1-1+b1 readline-common=8.0-4 rna-star=2.7.6a+dfsg-1 salmon=1.3.0+ds1-3 samtools=1.11-1 sed=4.7-1 sensible-utils=0.0.12+nmu1 sgml-base=1.30 shared-mime-info=2.0-1 snakemake=5.24.1-1 sphinx-common=3.2.1-2 sphinx-rtd-theme-common=0.5.0+dfsg-1 sysvinit-utils=2.96-5 tar=1.30+dfsg-7 trim-galore=0.6.6-1 ttf-bitstream-vera=1.10-8 tzdata=2020c-1 ucf=3.0043 unzip=6.0-25 util-linux=2.36-3+b1 x11-common=1:7.7+21 xdg-utils=1.1.3-2 xml-core=0.18+nmu1 xz-utils=5.2.4-1+b1 zip=3.0-11+b1 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201105T220209Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201021T204749Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d pigx-rnaseq=0.0.10+ds-2 && mkdir -p /build/pigx-rnaseq-EedzUM && dpkg-source --no-check -x /*.dsc /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds && chown -R builduser:builduser /build/pigx-rnaseq-EedzUM" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1603460552" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/pigx-rnaseq-EedzUM /tmp/pigx-rnaseq-0.0.10+ds-2388w1zvp bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201021T204749Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.7bDDTbtalT as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.7bDDTbtalT Reading package lists... Building dependency tree... util-linux is already the newest version (2.36-3+b1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20201021T204749Z unstable/main amd64 libfakeroot amd64 1.25.3-1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201021T204749Z unstable/main amd64 fakeroot amd64 1.25.3-1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (970 kB/s) Selecting previously unselected package libfakeroot: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 ... 4664 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1_amd64.deb ... Unpacking fakeroot (1.25.3-1) ... Setting up libfakeroot:amd64 (1.25.3-1) ... Setting up fakeroot (1.25.3-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201105T220209Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201021T204749Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.7bDDTbtalT Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201105T220209Z unstable InRelease [146 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201021T204749Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20201105T220209Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201105T220209Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201105T220209Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20201105T220209Z unstable/main amd64 Packages [11.5 MB] Fetched 34.2 MB in 29s (1187 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.7bDDTbtalT I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d pigx-rnaseq=0.0.10+ds-2 && mkdir -p /build/pigx-rnaseq-EedzUM && dpkg-source --no-check -x /*.dsc /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds && chown -R builduser:builduser /build/pigx-rnaseq-EedzUM"' exec /tmp/mmdebstrap.7bDDTbtalT Reading package lists... NOTICE: 'pigx-rnaseq' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/pigx-rnaseq.git Please use: git clone https://salsa.debian.org/med-team/pigx-rnaseq.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 7065 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main pigx-rnaseq 0.0.10+ds-2 (dsc) [2832 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main pigx-rnaseq 0.0.10+ds-2 (tar) [7057 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main pigx-rnaseq 0.0.10+ds-2 (diff) [5472 B] Fetched 7065 kB in 6s (1206 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'pigx-rnaseq_0.0.10+ds-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting pigx-rnaseq in /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds dpkg-source: info: unpacking pigx-rnaseq_0.0.10+ds.orig.tar.xz dpkg-source: info: unpacking pigx-rnaseq_0.0.10+ds-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying latencyWait.patch dpkg-source: info: applying notSelfContained.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1603460552" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.7bDDTbtalT dpkg-buildpackage: info: source package pigx-rnaseq dpkg-buildpackage: info: source version 0.0.10+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds' dh_auto_clean install -d /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10\+ds/debian/.debhelper/generated/_source/home 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/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds' 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 \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary-indep dh binary-indep dh_update_autotools_config -i dh_autoreconf -i 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 configure.ac:6: installing 'build-aux/install-sh' configure.ac:6: installing 'build-aux/missing' Makefile.am:16: warning: whitespace following trailing backslash 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 dh_auto_configure -i install -d /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10\+ds/debian/.debhelper/generated/_source/home ./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 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /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... 3.8 checking for python3 platform... linux checking for python3 script directory... ${prefix}/lib/python3.8/site-packages checking for python3 extension module directory... ${exec_prefix}/lib/python3.8/site-packages checking python3 module: yaml... yes checking for gunzip... /bin/gunzip 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 checking for pandoc-citeproc... /usr/bin/pandoc-citeproc configure: Using /usr/bin/fastqc as fastqc executable. configure: Using /usr/bin/trim_galore as trim_galore executable. configure: Using /usr/bin/STAR as STAR executable. checking for multiqc... /usr/bin/multiqc checking for htseq-count... /usr/bin/htseq-count configure: Using /usr/bin/salmon as salmon executable. checking for R... /usr/bin/R checking for Rscript... /usr/bin/Rscript 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 gProfileR ... 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 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_trim_galore/test.sh config.status: creating tests/test_star/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_fastqc/test.sh config.status: creating tests/test_star_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 dh_auto_build -i make -j4 make[1]: Entering directory '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds' debian/rules override_dh_auto_test make[1]: Entering directory '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds' 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: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Job counts: count jobs 1 all 1 collate_read_counts 6 count_reads 1 counts_from_SALMON 6 fastqc 6 genomeCoverage 6 index_bam 1 multiqc 1 norm_counts_deseq 1 report1 1 report2 1 report3 1 salmon_index 6 salmon_quant 6 sort_bam 1 star_index 6 star_map 1 translate_sample_sheet_for_report 4 trim_galore_pe 2 trim_galore_se 59 [Fri Oct 22 03:46:14 2021] rule trim_galore_se: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep3.read1.fastq.gz output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3_R.fastq.gz log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_UHR_Rep3.log jobid: 52 wildcards: sample=UHR_Rep3 /usr/bin/trim_galore -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep3.read1.fastq.gz >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_UHR_Rep3.log 2>&1 && sleep 10 && mv /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3.read1_trimmed.fq.gz /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3_R.fastq.gz [Fri Oct 22 03:46:26 2021] Finished job 52. 1 of 59 steps (2%) done [Fri Oct 22 03:46:26 2021] rule trim_galore_se: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep1.read1.fastq.gz output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1_R.fastq.gz log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_HBR_Rep1.log jobid: 47 wildcards: sample=HBR_Rep1 /usr/bin/trim_galore -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep1.read1.fastq.gz >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_HBR_Rep1.log 2>&1 && sleep 10 && mv /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1.read1_trimmed.fq.gz /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1_R.fastq.gz [Fri Oct 22 03:46:38 2021] Finished job 47. 2 of 59 steps (3%) done [Fri Oct 22 03:46:38 2021] rule trim_galore_pe: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep1.read1.fastq.gz, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep1.read2.fastq.gz output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R1.fastq.gz, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R2.fastq.gz log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_UHR_Rep1.log jobid: 50 wildcards: sample=UHR_Rep1 /usr/bin/trim_galore -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads --paired /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep1.read1.fastq.gz /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep1.read2.fastq.gz >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_UHR_Rep1.log 2>&1 && sleep 10 && mv /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1.read1_val_1.fq.gz /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R1.fastq.gz && mv /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1.read2_val_2.fq.gz /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R2.fastq.gz [Fri Oct 22 03:46:51 2021] Finished job 50. 3 of 59 steps (5%) done [Fri Oct 22 03:46:52 2021] rule trim_galore_pe: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep2.read1.fastq.gz, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R1.fastq.gz, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R2.fastq.gz log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_HBR_Rep2.log jobid: 48 wildcards: sample=HBR_Rep2 /usr/bin/trim_galore -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads --paired /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep2.read1.fastq.gz /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_HBR_Rep2.log 2>&1 && sleep 10 && mv /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2.read1_val_1.fq.gz /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R1.fastq.gz && mv /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2.read2_val_2.fq.gz /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R2.fastq.gz [Fri Oct 22 03:47:04 2021] Finished job 48. 4 of 59 steps (7%) done [Fri Oct 22 03:47:04 2021] rule trim_galore_pe: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep2.read1.fastq.gz, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep2.read2.fastq.gz output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R1.fastq.gz, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R2.fastq.gz log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_UHR_Rep2.log jobid: 51 wildcards: sample=UHR_Rep2 /usr/bin/trim_galore -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads --paired /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep2.read1.fastq.gz /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep2.read2.fastq.gz >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_UHR_Rep2.log 2>&1 && sleep 10 && mv /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2.read1_val_1.fq.gz /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R1.fastq.gz && mv /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2.read2_val_2.fq.gz /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R2.fastq.gz [Fri Oct 22 03:47:17 2021] Finished job 51. 5 of 59 steps (8%) done [Fri Oct 22 03:47:17 2021] rule trim_galore_pe: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep3.read1.fastq.gz, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep3.read2.fastq.gz output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R1.fastq.gz, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R2.fastq.gz log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_HBR_Rep3.log jobid: 49 wildcards: sample=HBR_Rep3 /usr/bin/trim_galore -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads --paired /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep3.read1.fastq.gz /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep3.read2.fastq.gz >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_HBR_Rep3.log 2>&1 && sleep 10 && mv /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3.read1_val_1.fq.gz /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R1.fastq.gz && mv /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3.read2_val_2.fq.gz /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R2.fastq.gz [Fri Oct 22 03:47:29 2021] Finished job 49. 6 of 59 steps (10%) done [Fri Oct 22 03:47:30 2021] rule translate_sample_sheet_for_report: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_sheet.csv output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv jobid: 34 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts//translate_sample_sheet_for_report.R /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_sheet.csv [Fri Oct 22 03:47:30 2021] Finished job 34. 7 of 59 steps (12%) done [Fri Oct 22 03:47:30 2021] rule salmon_index: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.cdna.fasta output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_index.log jobid: 2 /usr/bin/salmon index -t /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.cdna.fasta -i /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -p 8 >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_index.log 2>&1 [Fri Oct 22 03:48:31 2021] Finished job 2. 8 of 59 steps (14%) done [Fri Oct 22 03:48:31 2021] rule star_index: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.fasta output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_index.log jobid: 1 /usr/bin/STAR --runMode genomeGenerate --runThreadN 2 --genomeDir /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/star_index --genomeFastaFiles /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.fasta --sjdbGTFfile /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_index.log 2>&1 [Fri Oct 22 03:49:12 2021] Finished job 1. 9 of 59 steps (15%) done [Fri Oct 22 03:49:12 2021] rule star_map: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R1.fastq.gz, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R2.fastq.gz output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.out.bam log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_HBR_Rep2.log jobid: 54 wildcards: sample=HBR_Rep2 /usr/bin/STAR --runThreadN 2 --genomeDir /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/star_index --readFilesIn /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R1.fastq.gz /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R2.fastq.gz --readFilesCommand '/bin/gunzip -c' --outSAMtype BAM Unsorted --outFileNamePrefix /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_ >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_HBR_Rep2.log 2>&1 [Fri Oct 22 03:49:16 2021] Finished job 54. 10 of 59 steps (17%) done [Fri Oct 22 03:49:16 2021] rule star_map: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R1.fastq.gz, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R2.fastq.gz output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.out.bam log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_UHR_Rep2.log jobid: 57 wildcards: sample=UHR_Rep2 /usr/bin/STAR --runThreadN 2 --genomeDir /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/star_index --readFilesIn /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R1.fastq.gz /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R2.fastq.gz --readFilesCommand '/bin/gunzip -c' --outSAMtype BAM Unsorted --outFileNamePrefix /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_ >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_UHR_Rep2.log 2>&1 [Fri Oct 22 03:49:19 2021] Finished job 57. 11 of 59 steps (19%) done [Fri Oct 22 03:49:19 2021] rule star_map: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3_R.fastq.gz output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.out.bam log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_UHR_Rep3.log jobid: 58 wildcards: sample=UHR_Rep3 /usr/bin/STAR --runThreadN 2 --genomeDir /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/star_index --readFilesIn /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3_R.fastq.gz --readFilesCommand '/bin/gunzip -c' --outSAMtype BAM Unsorted --outFileNamePrefix /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_ >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_UHR_Rep3.log 2>&1 [Fri Oct 22 03:49:22 2021] Finished job 58. 12 of 59 steps (20%) done [Fri Oct 22 03:49:22 2021] rule star_map: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R1.fastq.gz, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R2.fastq.gz output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.out.bam log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_UHR_Rep1.log jobid: 56 wildcards: sample=UHR_Rep1 /usr/bin/STAR --runThreadN 2 --genomeDir /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/star_index --readFilesIn /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R1.fastq.gz /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R2.fastq.gz --readFilesCommand '/bin/gunzip -c' --outSAMtype BAM Unsorted --outFileNamePrefix /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_ >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_UHR_Rep1.log 2>&1 [Fri Oct 22 03:49:26 2021] Finished job 56. 13 of 59 steps (22%) done [Fri Oct 22 03:49:26 2021] rule star_map: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R1.fastq.gz, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R2.fastq.gz output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.out.bam log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_HBR_Rep3.log jobid: 55 wildcards: sample=HBR_Rep3 /usr/bin/STAR --runThreadN 2 --genomeDir /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/star_index --readFilesIn /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R1.fastq.gz /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R2.fastq.gz --readFilesCommand '/bin/gunzip -c' --outSAMtype BAM Unsorted --outFileNamePrefix /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_ >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_HBR_Rep3.log 2>&1 [Fri Oct 22 03:49:28 2021] Finished job 55. 14 of 59 steps (24%) done [Fri Oct 22 03:49:28 2021] rule star_map: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1_R.fastq.gz output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.out.bam log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_HBR_Rep1.log jobid: 53 wildcards: sample=HBR_Rep1 /usr/bin/STAR --runThreadN 2 --genomeDir /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/star_index --readFilesIn /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1_R.fastq.gz --readFilesCommand '/bin/gunzip -c' --outSAMtype BAM Unsorted --outFileNamePrefix /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_ >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_HBR_Rep1.log 2>&1 [Fri Oct 22 03:49:31 2021] Finished job 53. 15 of 59 steps (25%) done [Fri Oct 22 03:49:31 2021] rule sort_bam: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.out.bam output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_UHR_Rep2.log jobid: 26 wildcards: sample=UHR_Rep2 /usr/bin/samtools sort -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.out.bam >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_UHR_Rep2.log 2>&1 [Fri Oct 22 03:49:32 2021] Finished job 26. 16 of 59 steps (27%) done [Fri Oct 22 03:49:32 2021] rule sort_bam: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.out.bam output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_HBR_Rep3.log jobid: 24 wildcards: sample=HBR_Rep3 /usr/bin/samtools sort -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.out.bam >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_HBR_Rep3.log 2>&1 [Fri Oct 22 03:49:32 2021] Finished job 24. 17 of 59 steps (29%) done [Fri Oct 22 03:49:32 2021] rule sort_bam: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.out.bam output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_HBR_Rep2.log jobid: 23 wildcards: sample=HBR_Rep2 /usr/bin/samtools sort -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.out.bam >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_HBR_Rep2.log 2>&1 [Fri Oct 22 03:49:32 2021] Finished job 23. 18 of 59 steps (31%) done [Fri Oct 22 03:49:32 2021] rule sort_bam: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.out.bam output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_UHR_Rep3.log jobid: 27 wildcards: sample=UHR_Rep3 /usr/bin/samtools sort -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.out.bam >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_UHR_Rep3.log 2>&1 [Fri Oct 22 03:49:32 2021] Finished job 27. 19 of 59 steps (32%) done [Fri Oct 22 03:49:32 2021] rule fastqc: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/UHR_Rep3_Aligned.sortedByCoord.out_fastqc.zip log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_UHR_Rep3.log jobid: 33 wildcards: sample=UHR_Rep3 /usr/bin/fastqc -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/fastqc -f bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_UHR_Rep3.log 2>&1 [Fri Oct 22 03:49:59 2021] Finished job 33. 20 of 59 steps (34%) done [Fri Oct 22 03:49:59 2021] rule sort_bam: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.out.bam output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_UHR_Rep1.log jobid: 25 wildcards: sample=UHR_Rep1 /usr/bin/samtools sort -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.out.bam >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_UHR_Rep1.log 2>&1 [Fri Oct 22 03:49:59 2021] Finished job 25. 21 of 59 steps (36%) done [Fri Oct 22 03:49:59 2021] rule fastqc: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/UHR_Rep2_Aligned.sortedByCoord.out_fastqc.zip log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_UHR_Rep2.log jobid: 32 wildcards: sample=UHR_Rep2 /usr/bin/fastqc -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/fastqc -f bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_UHR_Rep2.log 2>&1 [Fri Oct 22 03:50:14 2021] Finished job 32. 22 of 59 steps (37%) done [Fri Oct 22 03:50:14 2021] rule sort_bam: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.out.bam output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_HBR_Rep1.log jobid: 22 wildcards: sample=HBR_Rep1 /usr/bin/samtools sort -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.out.bam >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_HBR_Rep1.log 2>&1 [Fri Oct 22 03:50:14 2021] Finished job 22. 23 of 59 steps (39%) done [Fri Oct 22 03:50:14 2021] rule fastqc: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/UHR_Rep1_Aligned.sortedByCoord.out_fastqc.zip log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_UHR_Rep1.log jobid: 31 wildcards: sample=UHR_Rep1 /usr/bin/fastqc -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/fastqc -f bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_UHR_Rep1.log 2>&1 [Fri Oct 22 03:50:33 2021] Finished job 31. 24 of 59 steps (41%) done [Fri Oct 22 03:50:33 2021] rule salmon_quant: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R1.fastq.gz, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R2.fastq.gz output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep2/quant.genes.sf log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_HBR_Rep2.log jobid: 17 wildcards: sample=HBR_Rep2 Job counts: count jobs 1 salmon_quant 1 /usr/bin/salmon quant -i /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -l A -p 8 -1 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R1.fastq.gz -2 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R2.fastq.gz -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep2 --seqBias --gcBias -g /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_HBR_Rep2.log 2>&1 [Fri Oct 22 03:50:36 2021] Finished job 17. 25 of 59 steps (42%) done [Fri Oct 22 03:50:36 2021] rule salmon_quant: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R1.fastq.gz, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R2.fastq.gz output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep1/quant.genes.sf log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_UHR_Rep1.log jobid: 19 wildcards: sample=UHR_Rep1 Job counts: count jobs 1 salmon_quant 1 /usr/bin/salmon quant -i /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -l A -p 8 -1 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R1.fastq.gz -2 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R2.fastq.gz -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep1 --seqBias --gcBias -g /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_UHR_Rep1.log 2>&1 [Fri Oct 22 03:50:39 2021] Finished job 19. 26 of 59 steps (44%) done [Fri Oct 22 03:50:39 2021] rule salmon_quant: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R1.fastq.gz, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R2.fastq.gz output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep2/quant.genes.sf log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_UHR_Rep2.log jobid: 20 wildcards: sample=UHR_Rep2 Job counts: count jobs 1 salmon_quant 1 /usr/bin/salmon quant -i /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -l A -p 8 -1 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R1.fastq.gz -2 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R2.fastq.gz -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep2 --seqBias --gcBias -g /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_UHR_Rep2.log 2>&1 [Fri Oct 22 03:50:43 2021] Finished job 20. 27 of 59 steps (46%) done [Fri Oct 22 03:50:43 2021] rule salmon_quant: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R1.fastq.gz, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R2.fastq.gz output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep3/quant.genes.sf log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_HBR_Rep3.log jobid: 18 wildcards: sample=HBR_Rep3 Job counts: count jobs 1 salmon_quant 1 /usr/bin/salmon quant -i /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -l A -p 8 -1 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R1.fastq.gz -2 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R2.fastq.gz -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep3 --seqBias --gcBias -g /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_HBR_Rep3.log 2>&1 [Fri Oct 22 03:50:47 2021] Finished job 18. 28 of 59 steps (47%) done [Fri Oct 22 03:50:47 2021] rule salmon_quant: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1_R.fastq.gz output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep1/quant.genes.sf log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_HBR_Rep1.log jobid: 16 wildcards: sample=HBR_Rep1 Job counts: count jobs 1 salmon_quant 1 /usr/bin/salmon quant -i /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -l A -p 8 -r /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1_R.fastq.gz -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep1 --seqBias --gcBias -g /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_HBR_Rep1.log 2>&1 [Fri Oct 22 03:50:50 2021] Finished job 16. 29 of 59 steps (49%) done [Fri Oct 22 03:50:50 2021] rule salmon_quant: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3_R.fastq.gz output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep3/quant.genes.sf log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_UHR_Rep3.log jobid: 21 wildcards: sample=UHR_Rep3 Job counts: count jobs 1 salmon_quant 1 /usr/bin/salmon quant -i /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -l A -p 8 -r /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3_R.fastq.gz -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep3 --seqBias --gcBias -g /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_UHR_Rep3.log 2>&1 [Fri Oct 22 03:50:53 2021] Finished job 21. 30 of 59 steps (51%) done [Fri Oct 22 03:50:53 2021] rule index_bam: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_UHR_Rep1.log jobid: 44 wildcards: sample=UHR_Rep1 /usr/bin/samtools index /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_UHR_Rep1.log 2>&1 [Fri Oct 22 03:50:53 2021] Finished job 44. 31 of 59 steps (53%) done [Fri Oct 22 03:50:53 2021] rule index_bam: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_HBR_Rep2.log jobid: 42 wildcards: sample=HBR_Rep2 /usr/bin/samtools index /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_HBR_Rep2.log 2>&1 [Fri Oct 22 03:50:53 2021] Finished job 42. 32 of 59 steps (54%) done [Fri Oct 22 03:50:53 2021] rule index_bam: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_HBR_Rep3.log jobid: 43 wildcards: sample=HBR_Rep3 /usr/bin/samtools index /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_HBR_Rep3.log 2>&1 [Fri Oct 22 03:50:53 2021] Finished job 43. 33 of 59 steps (56%) done [Fri Oct 22 03:50:53 2021] rule index_bam: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_UHR_Rep3.log jobid: 46 wildcards: sample=UHR_Rep3 /usr/bin/samtools index /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_UHR_Rep3.log 2>&1 [Fri Oct 22 03:50:53 2021] Finished job 46. 34 of 59 steps (58%) done [Fri Oct 22 03:50:53 2021] rule index_bam: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_HBR_Rep1.log jobid: 41 wildcards: sample=HBR_Rep1 /usr/bin/samtools index /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_HBR_Rep1.log 2>&1 [Fri Oct 22 03:50:53 2021] Finished job 41. 35 of 59 steps (59%) done [Fri Oct 22 03:50:53 2021] rule index_bam: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_UHR_Rep2.log jobid: 45 wildcards: sample=UHR_Rep2 /usr/bin/samtools index /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_UHR_Rep2.log 2>&1 [Fri Oct 22 03:50:53 2021] Finished job 45. 36 of 59 steps (61%) done [Fri Oct 22 03:50:53 2021] rule fastqc: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/HBR_Rep2_Aligned.sortedByCoord.out_fastqc.zip log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_HBR_Rep2.log jobid: 29 wildcards: sample=HBR_Rep2 /usr/bin/fastqc -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/fastqc -f bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_HBR_Rep2.log 2>&1 [Fri Oct 22 03:51:08 2021] Finished job 29. 37 of 59 steps (63%) done [Fri Oct 22 03:51:08 2021] rule fastqc: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/HBR_Rep3_Aligned.sortedByCoord.out_fastqc.zip log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_HBR_Rep3.log jobid: 30 wildcards: sample=HBR_Rep3 /usr/bin/fastqc -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/fastqc -f bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_HBR_Rep3.log 2>&1 [Fri Oct 22 03:51:22 2021] Finished job 30. 38 of 59 steps (64%) done [Fri Oct 22 03:51:22 2021] rule fastqc: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/HBR_Rep1_Aligned.sortedByCoord.out_fastqc.zip log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_HBR_Rep1.log jobid: 28 wildcards: sample=HBR_Rep1 /usr/bin/fastqc -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/fastqc -f bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_HBR_Rep1.log 2>&1 [Fri Oct 22 03:51:45 2021] Finished job 28. 39 of 59 steps (66%) done [Fri Oct 22 03:51:45 2021] rule multiqc: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/HBR_Rep1_Aligned.sortedByCoord.out_fastqc.zip, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/HBR_Rep2_Aligned.sortedByCoord.out_fastqc.zip, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/HBR_Rep3_Aligned.sortedByCoord.out_fastqc.zip, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/UHR_Rep1_Aligned.sortedByCoord.out_fastqc.zip, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/UHR_Rep2_Aligned.sortedByCoord.out_fastqc.zip, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/UHR_Rep3_Aligned.sortedByCoord.out_fastqc.zip output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/multiqc/multiqc_report.html log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/multiqc.log jobid: 3 /usr/bin/multiqc -o /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/multiqc /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/multiqc.log 2>&1 [Fri Oct 22 03:52:02 2021] Finished job 3. 40 of 59 steps (68%) done [Fri Oct 22 03:52:02 2021] rule counts_from_SALMON: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/TPM_counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/TPM_counts_from_SALMON.genes.tsv log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_import_counts.log jobid: 4 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts//counts_matrix_from_SALMON.R /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_import_counts.log 2>&1 [Fri Oct 22 03:52:24 2021] Finished job 4. 41 of 59 steps (69%) done [Fri Oct 22 03:52:24 2021] rule report3: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.salmon.genes.deseq.report.html log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/analysis1.report.salmon.genes.log jobid: 15 wildcards: analysis=analysis1 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts/runDeseqReport.R --logo=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/images/Logo_PiGx.png --prefix='analysis1.salmon.genes' --reportFile=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts/deseqReport.Rmd --countDataFile=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.genes.tsv --colDataFile=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv --gtfFile=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/report --organism='' --selfContained=FALSE >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/analysis1.report.salmon.genes.log 2>&1 [Fri Oct 22 03:53:14 2021] Finished job 15. 42 of 59 steps (71%) done [Fri Oct 22 03:53:14 2021] rule report2: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.salmon.transcripts.deseq.report.html log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/analysis1.report.salmon.transcripts.log jobid: 14 wildcards: analysis=analysis1 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts/runDeseqReport.R --logo=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/images/Logo_PiGx.png --prefix='analysis1.salmon.transcripts' --reportFile=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts/deseqReport.Rmd --countDataFile=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.transcripts.tsv --colDataFile=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv --gtfFile=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/report --organism='' >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/analysis1.report.salmon.transcripts.log 2>&1 [Fri Oct 22 03:54:08 2021] Finished job 14. 43 of 59 steps (73%) done [Fri Oct 22 03:54:08 2021] rule count_reads: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1.read_counts.csv log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/UHR_Rep1.count_reads.log jobid: 38 wildcards: sample=UHR_Rep1 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts//count_reads.R UHR_Rep1 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/UHR_Rep1.count_reads.log 2>&1 [Fri Oct 22 03:54:30 2021] Finished job 38. 44 of 59 steps (75%) done [Fri Oct 22 03:54:30 2021] rule count_reads: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2.read_counts.csv log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/HBR_Rep2.count_reads.log jobid: 36 wildcards: sample=HBR_Rep2 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts//count_reads.R HBR_Rep2 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/HBR_Rep2.count_reads.log 2>&1 [Fri Oct 22 03:54:52 2021] Finished job 36. 45 of 59 steps (76%) done [Fri Oct 22 03:54:52 2021] rule count_reads: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3.read_counts.csv log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/UHR_Rep3.count_reads.log jobid: 40 wildcards: sample=UHR_Rep3 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts//count_reads.R UHR_Rep3 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/UHR_Rep3.count_reads.log 2>&1 [Fri Oct 22 03:55:16 2021] Finished job 40. 46 of 59 steps (78%) done [Fri Oct 22 03:55:16 2021] rule count_reads: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1.read_counts.csv log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/HBR_Rep1.count_reads.log jobid: 35 wildcards: sample=HBR_Rep1 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts//count_reads.R HBR_Rep1 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/HBR_Rep1.count_reads.log 2>&1 [Fri Oct 22 03:55:37 2021] Finished job 35. 47 of 59 steps (80%) done [Fri Oct 22 03:55:37 2021] rule count_reads: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2.read_counts.csv log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/UHR_Rep2.count_reads.log jobid: 39 wildcards: sample=UHR_Rep2 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts//count_reads.R UHR_Rep2 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/UHR_Rep2.count_reads.log 2>&1 [Fri Oct 22 03:56:00 2021] Finished job 39. 48 of 59 steps (81%) done [Fri Oct 22 03:56:00 2021] rule count_reads: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3.read_counts.csv log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/HBR_Rep3.count_reads.log jobid: 37 wildcards: sample=HBR_Rep3 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts//count_reads.R HBR_Rep3 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/HBR_Rep3.count_reads.log 2>&1 [Fri Oct 22 03:56:24 2021] Finished job 37. 49 of 59 steps (83%) done [Fri Oct 22 03:56:24 2021] rule collate_read_counts: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1.read_counts.csv, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2.read_counts.csv, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3.read_counts.csv, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1.read_counts.csv, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2.read_counts.csv, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3.read_counts.csv output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/collate_read_counts.log jobid: 5 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts/collate_read_counts.R /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/collate_read_counts.log 2>&1 [Fri Oct 22 03:56:25 2021] Finished job 5. 50 of 59 steps (85%) done [Fri Oct 22 03:56:25 2021] rule norm_counts_deseq: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_normalized_counts.tsv log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/norm_counts_deseq.log jobid: 6 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts/norm_counts_deseq.R /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/norm_counts_deseq.log 2>&1 [Fri Oct 22 03:56:47 2021] Finished job 6. 51 of 59 steps (86%) done [Fri Oct 22 03:56:47 2021] rule report1: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.star.deseq.report.html log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/analysis1.report.star.log jobid: 13 wildcards: analysis=analysis1 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts/runDeseqReport.R --logo=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/images/Logo_PiGx.png --prefix='analysis1.star' --reportFile=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts/deseqReport.Rmd --countDataFile=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv --colDataFile=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv --gtfFile=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/report --organism='' >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/analysis1.report.star.log 2>&1 [Fri Oct 22 03:57:40 2021] Finished job 13. 52 of 59 steps (88%) done [Fri Oct 22 03:57:40 2021] rule genomeCoverage: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep1.forward.bigwig, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep1.reverse.bigwig log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_HBR_Rep1.log jobid: 7 wildcards: sample=HBR_Rep1 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts//export_bigwig.R /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam HBR_Rep1 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_HBR_Rep1.log 2>&1 [Fri Oct 22 03:57:59 2021] Finished job 7. 53 of 59 steps (90%) done [Fri Oct 22 03:57:59 2021] rule genomeCoverage: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep3.forward.bigwig, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep3.reverse.bigwig log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_HBR_Rep3.log jobid: 9 wildcards: sample=HBR_Rep3 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts//export_bigwig.R /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam HBR_Rep3 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_HBR_Rep3.log 2>&1 [Fri Oct 22 03:58:18 2021] Finished job 9. 54 of 59 steps (92%) done [Fri Oct 22 03:58:18 2021] rule genomeCoverage: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep1.forward.bigwig, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep1.reverse.bigwig log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_UHR_Rep1.log jobid: 10 wildcards: sample=UHR_Rep1 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts//export_bigwig.R /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam UHR_Rep1 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_UHR_Rep1.log 2>&1 [Fri Oct 22 03:58:36 2021] Finished job 10. 55 of 59 steps (93%) done [Fri Oct 22 03:58:36 2021] rule genomeCoverage: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep2.forward.bigwig, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep2.reverse.bigwig log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_UHR_Rep2.log jobid: 11 wildcards: sample=UHR_Rep2 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts//export_bigwig.R /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam UHR_Rep2 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_UHR_Rep2.log 2>&1 [Fri Oct 22 03:58:53 2021] Finished job 11. 56 of 59 steps (95%) done [Fri Oct 22 03:58:53 2021] rule genomeCoverage: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep3.forward.bigwig, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep3.reverse.bigwig log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_UHR_Rep3.log jobid: 12 wildcards: sample=UHR_Rep3 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts//export_bigwig.R /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam UHR_Rep3 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_UHR_Rep3.log 2>&1 [Fri Oct 22 03:59:12 2021] Finished job 12. 57 of 59 steps (97%) done [Fri Oct 22 03:59:12 2021] rule genomeCoverage: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep2.forward.bigwig, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep2.reverse.bigwig log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_HBR_Rep2.log jobid: 8 wildcards: sample=HBR_Rep2 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/scripts//export_bigwig.R /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam HBR_Rep2 /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files >> /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_HBR_Rep2.log 2>&1 [Fri Oct 22 03:59:31 2021] Finished job 8. 58 of 59 steps (98%) done [Fri Oct 22 03:59:32 2021] localrule all: input: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/multiqc/multiqc_report.html, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/TPM_counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/TPM_counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep1.forward.bigwig, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep2.forward.bigwig, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep3.forward.bigwig, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep1.forward.bigwig, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep2.forward.bigwig, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep3.forward.bigwig, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep1.reverse.bigwig, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep2.reverse.bigwig, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep3.reverse.bigwig, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep1.reverse.bigwig, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep2.reverse.bigwig, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep3.reverse.bigwig, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.star.deseq.report.html, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.salmon.transcripts.deseq.report.html, /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.salmon.genes.deseq.report.html jobid: 0 [Fri Oct 22 03:59:32 2021] Finished job 0. 59 of 59 steps (100%) done Complete log: /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/.snakemake/log/2021-10-22T034613.770731.snakemake.log The following files have been generated: - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/multiqc/multiqc_report.html - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.transcripts.tsv - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.genes.tsv - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/TPM_counts_from_SALMON.transcripts.tsv - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/TPM_counts_from_SALMON.genes.tsv - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep1.forward.bigwig - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep2.forward.bigwig - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep3.forward.bigwig - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep1.forward.bigwig - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep2.forward.bigwig - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep3.forward.bigwig - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep1.reverse.bigwig - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep2.reverse.bigwig - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep3.reverse.bigwig - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep1.reverse.bigwig - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep2.reverse.bigwig - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep3.reverse.bigwig - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.star.deseq.report.html - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.salmon.transcripts.deseq.report.html - /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.salmon.genes.deseq.report.html make[1]: Leaving directory '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds' create-stamp debian/debhelper-build-stamp dh_testroot -i dh_prep -i rm -f -- debian/pigx-rnaseq.substvars rm -fr -- debian/.debhelper/generated/pigx-rnaseq/ debian/pigx-rnaseq/ debian/tmp/ debian/rules override_dh_auto_install make[1]: Entering directory '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds' dh_auto_install install -d /build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10\+ds/debian/pigx-rnaseq make -j4 install DESTDIR=/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10\+ds/debian/pigx-rnaseq AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds' make[3]: Entering directory '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds' /bin/mkdir -p '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' /bin/mkdir -p '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' /bin/mkdir -p '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/bin' /bin/mkdir -p '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' /usr/bin/install -c pigx_rnaseq.py qsub-template.sh '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' /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/export_bigwig.R scripts/norm_counts_deseq.R scripts/count_reads.R scripts/collate_read_counts.R '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' /usr/bin/install -c pigx-rnaseq '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/bin' /usr/bin/install -c -m 644 README.md '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' /bin/mkdir -p '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/share/pigx_rnaseq' /usr/bin/install -c -m 644 etc/sample_sheet.csv.example etc/settings.yaml etc/pretty.txt images/Logo_PiGx.png '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/share/pigx_rnaseq' make[3]: Leaving directory '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds' make[2]: Leaving directory '/build/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds' 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/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds' dh_installdocs -i install -d debian/pigx-rnaseq/usr/share/doc/pigx-rnaseq install -d debian/.debhelper/generated/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 -i install -p -m0644 debian/changelog debian/pigx-rnaseq/usr/share/doc/pigx-rnaseq/changelog.Debian dh_installman -i install -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 -i dh_link -i dh_strip_nondeterminism -i Using 1603460552 as canonical time Normalizing debian/pigx-rnaseq/usr/share/pigx_rnaseq/Logo_PiGx.png using File::StripNondeterminism::handlers::png dh_compress -i 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/pigx-rnaseq-EedzUM/pigx-rnaseq-0.0.10+ds' dh_fixperms -i 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 -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing -i dh_installdeb -i install -d debian/pigx-rnaseq/DEBIAN dh_gencontrol -i 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 -Pdebian/pigx-rnaseq chmod 0644 -- debian/pigx-rnaseq/DEBIAN/control dh_md5sums -i 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 -i dpkg-deb --root-owner-group --build debian/pigx-rnaseq .. dpkg-deb: building package 'pigx-rnaseq' in '../pigx-rnaseq_0.0.10+ds-2_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../pigx-rnaseq_0.0.10+ds-2_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/pigx-rnaseq-EedzUM /tmp/pigx-rnaseq-0.0.10+ds-2388w1zvp I: cleaning package lists and apt cache... W: deleting files in /tmp: hsperfdata_builduser W: deleting files in /tmp: hsperfdata_root I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.7bDDTbtalT... I: success in 2102.4591 seconds md5: pigx-rnaseq_0.0.10+ds-2_all.deb: OK sha1: pigx-rnaseq_0.0.10+ds-2_all.deb: OK sha256: pigx-rnaseq_0.0.10+ds-2_all.deb: OK Checksums: OK