0s autopkgtest [17:36:56]: starting date and time: 2024-11-02 17:36:56+0000 0s autopkgtest [17:36:56]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [17:36:56]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.my_akys4/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:liburi-perl --apt-upgrade trinityrnaseq --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=liburi-perl/5.30-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-3.secgroup --name adt-plucky-amd64-trinityrnaseq-20241102-170137-juju-7f2275-prod-proposed-migration-environment-2-4ebdd19d-d423-489e-865f-47c430b49833 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 50s autopkgtest [17:37:46]: testbed dpkg architecture: amd64 50s autopkgtest [17:37:46]: testbed apt version: 2.9.8 50s autopkgtest [17:37:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup 50s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 50s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 50s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [40.4 kB] 50s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2480 kB] 50s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [175 kB] 50s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [235 kB] 50s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [163 kB] 50s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 50s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [1856 kB] 50s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [928 kB] 50s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [22.0 kB] 50s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [68.4 kB] 51s Fetched 6082 kB in 1s (8443 kB/s) 51s Reading package lists... 53s Reading package lists... 53s Building dependency tree... 53s Reading state information... 54s Calculating upgrade... 54s The following packages will be upgraded: 54s python3-zipp 54s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s Need to get 10.1 kB of archives. 54s After this operation, 2048 B disk space will be freed. 54s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-zipp all 3.20.2-1 [10.1 kB] 55s Fetched 10.1 kB in 0s (468 kB/s) 55s (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 ... 75323 files and directories currently installed.) 55s Preparing to unpack .../python3-zipp_3.20.2-1_all.deb ... 55s Unpacking python3-zipp (3.20.2-1) over (3.20.0-1) ... 55s Setting up python3-zipp (3.20.2-1) ... 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 57s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 57s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 57s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 57s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 57s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 58s Reading package lists... 58s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Calculating upgrade... 60s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s Reading package lists... 60s Building dependency tree... 60s Reading state information... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 62s autopkgtest [17:37:58]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 62s autopkgtest [17:37:58]: @@@@@@@@@@@@@@@@@@@@ apt-source trinityrnaseq 67s Get:1 http://ftpmaster.internal/ubuntu plucky/universe trinityrnaseq 2.15.1+dfsg-5build1 (dsc) [2629 B] 67s Get:2 http://ftpmaster.internal/ubuntu plucky/universe trinityrnaseq 2.15.1+dfsg-5build1 (tar) [307 MB] 67s Get:3 http://ftpmaster.internal/ubuntu plucky/universe trinityrnaseq 2.15.1+dfsg-5build1 (diff) [39.4 kB] 68s gpgv: Signature made Sun Apr 14 18:57:26 2024 UTC 68s gpgv: using RSA key AC0A4FF12611B6FCCF01C111393587D97D86500B 68s gpgv: Can't check signature: No public key 68s dpkg-source: warning: cannot verify inline signature for ./trinityrnaseq_2.15.1+dfsg-5build1.dsc: no acceptable signature found 76s autopkgtest [17:38:12]: testing package trinityrnaseq version 2.15.1+dfsg-5build1 76s autopkgtest [17:38:12]: build not needed 79s autopkgtest [17:38:15]: test run-tests: preparing testbed 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 81s Starting pkgProblemResolver with broken count: 0 81s Starting 2 pkgProblemResolver with broken count: 0 81s Done 81s The following additional packages will be installed: 81s adwaita-icon-theme at-spi2-common berkeley-express bowtie bowtie2 81s ca-certificates-java dconf-gsettings-backend dconf-service default-jre 81s default-jre-headless fontconfig fontconfig-config fonts-dejavu-core 81s fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings 81s fonts-lmodern fonts-mathjax gtk-update-icon-cache hicolor-icon-theme hisat2 81s humanity-icon-theme jaligner java-common javascript-common jellyfish 81s kallisto libapache-pom-java libasan8 libasound2-data libasound2t64 81s libatinject-jsr330-api-java libatk-bridge2.0-0t64 libatk1.0-0t64 81s libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 81s libbamtools2.5.2 libbarclay-java libbibtex-parser-perl libblas3 libboost-dev 81s libboost-filesystem1.83.0 libboost-iostreams1.83.0 81s libboost-program-options1.83.0 libboost-thread1.83.0 libboost1.83-dev 81s libcairo-gobject2 libcairo2 libclone-perl libcolord2 libcommons-codec-java 81s libcommons-compress-java libcommons-io-java libcommons-jexl2-java 81s libcommons-lang3-java libcommons-logging-java libcommons-math3-java 81s libcommons-parent-java libcups2t64 libdatrie1 libdconf1 libdeflate0 81s libdrm-amdgpu1 libdrm-intel1 libdrm-radeon1 libencode-locale-perl libepoxy0 81s liberror-prone-java libfile-listing-perl libfontconfig1 libfreemarker-java 81s libgatk-native-bindings-java libgbm1 libgcc-14-dev libgdk-pixbuf-2.0-0 81s libgdk-pixbuf2.0-common libgetopt-java libgfortran5 libgif7 libgkl-java 81s libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 81s libgoogle-gson-java libgraphite2-3 libgtk-3-0t64 libgtk-3-common 81s libguava-java libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl 81s libhtml-tree-perl libhts3t64 libhtscodecs2 libhtsjdk-java 81s libhttp-cookies-perl libhttp-date-perl libhttp-message-perl 81s libhttp-negotiate-perl libhttpclient-java libhttpcore-java libhwasan0 81s libhwloc15 libice6 libio-html-perl libio-socket-ssl-perl libio-string-perl 81s libitm1 libjbig0 libjbzip2-java libjellyfish-2.0-2 libjemalloc2 81s libjoptsimple-java libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootstrap4 81s libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery 81s libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json 81s libjs-lunr libjs-mathjax libjs-microplugin.js libjs-modernizr 81s libjs-popper.js libjs-prettify libjs-sifter.js libjs-sphinxdoc 81s libjs-twitter-bootstrap-datepicker libjs-underscore libjsr305-java 81s libjung-free-java libkpathsea6 liblapack3 liblatex-tounicode-perl liblcms2-2 81s liblerc4 liblightcouch-java liblog4j2-java liblsan0 liblua5.4-0 81s liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto7t64 81s libmbedtls14t64 libmbedx509-1t64 libmjson-java libmongodb-java libmpfi0 81s libncbi-ngs3 libncbi-vdb3 libnet-http-perl libnet-ssleay-perl libngs-java 81s libngs-jni libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 81s libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libpicard-java 81s libpixman-1-0 libpotrace0 libprotobuf32t64 libptexenc1 libquadmath0 81s librhino-java libsharpyuv0 libslf4j-java libsm6 libsnappy-java libsnappy-jni 81s libsnappy1v5 libstaden-read14t64 libstdc++-14-dev libsynctex2 libtbb12 81s libtbbbind-2-5 libtbbmalloc2 libtcl8.6 libteckit0 libtexlua53-5 libthai-data 81s libthai0 libtiff6 libtimedate-perl libtk8.6 libtry-tiny-perl libtsan2 81s libubsan1 liburi-perl libvulkan1 libwayland-client0 libwayland-cursor0 81s libwayland-egl1 libwayland-server0 libwebp7 libwww-perl 81s libwww-robotrules-perl libx11-xcb1 libxaw7 libxcb-dri2-0 libxcb-dri3-0 81s libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 81s libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxcursor1 libxdamage1 81s libxfixes3 libxft2 libxi6 libxinerama1 libxmu6 libxpm4 libxrandr2 81s libxrender1 libxshmfence1 libxss1 libxt6t64 libxtst6 libxxf86vm1 81s libzzip-0-13t64 littler mesa-libgallium ncbi-blast+ ncbi-data ncbi-vdb-data 81s node-bootstrap-sass node-html5shiv node-normalize.css openjdk-21-jre 81s openjdk-21-jre-headless pandoc pandoc-data parafly perl-openssl-defaults 81s python3-hisat2 python3-htseq python3-numpy python3-pysam r-base-core 81s r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache 81s r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biocstyle 81s r-bioc-biocversion r-bioc-biomart r-bioc-biostrings r-bioc-delayedarray 81s r-bioc-deseq2 r-bioc-dexseq r-bioc-edger r-bioc-genefilter 81s r-bioc-genelendatabase r-bioc-geneplotter r-bioc-genomeinfodb 81s r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures 81s r-bioc-genomicranges r-bioc-go.db r-bioc-goseq r-bioc-iranges 81s r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics r-bioc-qvalue 81s r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays 81s r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment 81s r-bioc-txdbmaker r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc 81s r-cran-abind r-cran-argparse r-cran-askpass r-cran-backports 81s r-cran-base64enc r-cran-bh r-cran-biasedurn r-cran-biocmanager r-cran-bit 81s r-cran-bit64 r-cran-bitops r-cran-blob r-cran-bookdown r-cran-broom 81s r-cran-bslib r-cran-cachem r-cran-callr r-cran-cellranger r-cran-cli 81s r-cran-clipr r-cran-cluster r-cran-codetools r-cran-colorspace 81s r-cran-commonmark r-cran-conflicted r-cran-cpp11 r-cran-crayon r-cran-curl 81s r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr 81s r-cran-dtplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver 81s r-cran-fastcluster r-cran-fastmap r-cran-filelock r-cran-findpython 81s r-cran-fontawesome r-cran-forcats r-cran-formatr r-cran-fs 81s r-cran-futile.logger r-cran-futile.options r-cran-gargle r-cran-generics 81s r-cran-ggdendro r-cran-ggplot2 r-cran-glue r-cran-googledrive 81s r-cran-googlesheets4 r-cran-goplot r-cran-gridextra r-cran-gtable 81s r-cran-haven r-cran-highr r-cran-hms r-cran-htmltools r-cran-httpuv 81s r-cran-httr r-cran-httr2 r-cran-hwriter r-cran-ids r-cran-isoband 81s r-cran-jquerylib r-cran-jsonlite r-cran-kernsmooth r-cran-knitr 81s r-cran-labeling r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lifecycle 81s r-cran-littler r-cran-locfit r-cran-lubridate r-cran-magrittr r-cran-mass 81s r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime 81s r-cran-modelr r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar 81s r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-plyr r-cran-png 81s r-cran-prettyunits r-cran-processx r-cran-progress r-cran-promises r-cran-ps 81s r-cran-purrr r-cran-r6 r-cran-ragg r-cran-rappdirs r-cran-rcolorbrewer 81s r-cran-rcpp r-cran-rcpparmadillo r-cran-rcurl r-cran-readr r-cran-readxl 81s r-cran-rematch r-cran-rematch2 r-cran-reprex r-cran-reshape2 r-cran-restfulr 81s r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-rstudioapi 81s r-cran-rvest r-cran-sass r-cran-scales r-cran-selectr r-cran-shiny 81s r-cran-snow r-cran-sourcetools r-cran-statmod r-cran-stringi r-cran-stringr 81s r-cran-survival r-cran-sys r-cran-systemfonts r-cran-textshaping 81s r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tidyverse 81s r-cran-timechange r-cran-tinytex r-cran-tzdb r-cran-utf8 r-cran-uuid 81s r-cran-vctrs r-cran-viridislite r-cran-vroom r-cran-withr r-cran-xfun 81s r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml rsem salmon samtools 81s subread t1utils tex-common texlive-base texlive-bibtex-extra 81s texlive-binaries texlive-latex-base trimmomatic trinityrnaseq 81s trinityrnaseq-examples ubuntu-mono unzip x11-common xdg-utils zip zlib1g-dev 81s Suggested packages: 81s bowtie-examples bowtie2-examples apache2 | lighttpd | httpd alsa-utils 81s libasound2-plugins libatinject-jsr330-api-java-doc libboost-doc 81s libboost1.83-doc libboost-atomic1.83-dev libboost-chrono1.83-dev 81s libboost-container1.83-dev libboost-context1.83-dev 81s libboost-contract1.83-dev libboost-coroutine1.83-dev 81s libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev 81s libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev 81s libboost-graph1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev 81s libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev 81s libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev 81s libboost-numpy1.83-dev libboost-program-options1.83-dev 81s libboost-python1.83-dev libboost-random1.83-dev libboost-regex1.83-dev 81s libboost-serialization1.83-dev libboost-stacktrace1.83-dev 81s libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev 81s libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev 81s libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev 81s colord libasm-java libxz-java libavalon-framework-java 81s libexcalibur-logkit-java liblog4j1.2-java cups-common jython libdom4j-java 81s libjaxen-java libjdom1-java libxalan2-java libgoogle-gson-java-doc gvfs 81s libdata-dump-perl picard-tools libio-compress-brotli-perl 81s libhwloc-contrib-plugins libjoptsimple-java-doc libjs-jquery-ui-docs 81s fonts-mathjax-extras fonts-stix libjs-mathjax-doc libjsr305-java-doc 81s liblcms2-utils libactivation-java libcommons-csv-java 81s libconversant-disruptor-java libdisruptor-java libgeronimo-jms-1.1-spec-java 81s libjackson2-dataformat-xml-java libjackson2-dataformat-yaml libjansi-java 81s libjctools-java libjeromq-java libmail-java libwoodstox-java 81s libcrypt-ssleay-perl libmpfi-doc libngs-java-doc pcscd rhino 81s libstdc++-14-doc tcl8.6 tk8.6 libsub-name-perl libbusiness-isbn-perl 81s libmime-base32-perl libregexp-ipv6-perl libauthen-ntlm-perl nodejs 81s libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 81s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic texlive-latex-recommended 81s texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra context 81s wkhtmltopdf librsvg2-bin groff ghc php python ruby libjs-katex 81s citation-style-language-styles debhelper gcc gfortran python-numpy-doc 81s python3-dev python3-pytest elpa-ess r-doc-info | r-doc-pdf r-mathlib 81s r-base-html r-bioc-org.hs.eg.db r-cran-runit r-bioc-graph r-bioc-all 81s r-cran-testthat r-bioc-affy r-cran-foreach r-cran-bbmisc r-cran-doparallel 81s r-bioc-variantannotation r-bioc-shortread r-cran-batchtools r-cran-mockery 81s r-cran-httptest2 r-bioc-bsgenome r-bioc-pwalign r-bioc-hdf5array 81s r-cran-lobstr r-bioc-delayedmatrixstats r-cran-pheatmap r-bioc-tximport 81s r-bioc-tximeta r-bioc-tximportdata r-cran-pbapply r-bioc-glmgampoi 81s r-cran-roxygen2 r-bioc-rhdf5 r-cran-seuratobject r-cran-class r-cran-r.utils 81s r-bioc-ensembldb r-bioc-annotationfilter r-cran-markdown r-bioc-gviz 81s r-bioc-annotationhub r-cran-ellipse r-cran-gplots r-bioc-sparsematrixstats 81s r-cran-rmariadb r-cran-ff r-cran-covr r-cran-kernlab r-cran-mvtnorm 81s r-cran-vcd r-cran-shinyjs r-cran-jpeg r-cran-viridis r-cran-rmysql 81s r-cran-bench r-cran-waldo r-cran-reticulate r-cran-spelling r-cran-magick 81s r-cran-sf r-cran-getopt r-cran-interp r-cran-gam r-cran-formattable 81s r-cran-nanotime r-cran-palmerpenguins r-cran-units r-cran-vdiffr 81s r-cran-inline r-cran-rmpi r-cran-rlecuyer r-cran-brio r-cran-here 81s r-cran-pkgbuild r-cran-pkgload r-cran-mockr r-cran-plm r-cran-zoo 81s r-bioc-ebseq cwltool ghostscript gv | postscript-viewer perl-tk xpdf 81s | pdf-viewer xzdec texlive-binaries-sse2 hintview texlive-latex-base-doc 81s wp2latex collectl transdecoder 81s Recommended packages: 81s librsvg2-common med-config bcftools alsa-ucm-conf alsa-topology-conf 81s at-spi2-core libgdk-pixbuf2.0-bin libgkl-jni libgl1-amber-dri libgtk-3-bin 81s libhtml-format-perl libhwloc-plugins node-jquery mesa-vulkan-drivers 81s | vulkan-icd libdata-dump-perl libhtml-form-perl libhttp-daemon-perl 81s libmailtools-perl libatk-wrapper-java-jni fonts-dejavu-extra r-recommended 81s r-base-dev r-doc-html r-cran-testthat r-cran-remotes r-cran-downlit 81s r-cran-htmlwidgets r-cran-miniui r-cran-rsconnect r-cran-testit r-cran-tufte 81s r-cran-webshot r-cran-aer r-cran-bbmle r-cran-boot r-cran-car r-cran-cardata 81s r-cran-caret r-cran-cmprsk r-cran-coda r-cran-covr r-cran-e1071 81s r-cran-emmeans r-cran-epir r-cran-gam r-cran-gee r-cran-geepack 81s r-cran-glmnet r-cran-gmm r-cran-hmisc r-cran-irlba r-cran-interp r-cran-ks 81s r-cran-lavaan r-cran-leaps r-cran-lme4 r-cran-lmtest r-cran-lsmeans 81s r-cran-maps r-cran-mclust r-cran-metafor r-cran-modeldata r-cran-multcomp 81s r-cran-network r-cran-nnet r-cran-ordinal r-cran-plm r-cran-psych 81s r-cran-quantreg r-cran-robust r-cran-robustbase r-cran-rsample 81s r-cran-sandwich r-cran-spdep r-cran-spatialreg r-cran-spelling r-cran-survey 81s r-cran-systemfit r-cran-tseries r-cran-zoo r-cran-future r-cran-thematic 81s r-cran-mockery r-cran-rprojroot r-cran-whoami r-cran-pkgload r-cran-bench 81s r-cran-brio r-cran-decor r-cran-desc r-cran-lobstr r-cran-webutils 81s r-cran-r.utils r-cran-xts r-cran-markdown r-cran-rpostgresql r-cran-rmysql 81s r-cran-unitizer r-cran-rsvg r-cran-sodium r-cran-rpart r-cran-hexbin 81s r-cran-mapproj r-cran-profvis r-cran-sf r-cran-svglite r-cran-vdiffr 81s r-cran-waldo r-cran-mockr r-cran-cairo r-cran-jpeg r-cran-docopt 81s r-cran-webfakes r-cran-r.rsp r-cran-gridsvg r-cran-magick r-cran-reticulate 81s r-cran-rgl r-cran-tikzdevice node-highlight.js r-cran-lintr r-cran-r.devices 81s r-cran-doparallel r-cran-foreach r-cran-iterators r-cran-itertools 81s r-cran-pingr r-cran-sessioninfo r-cran-runit r-cran-usethis r-cran-dygraphs 81s r-cran-dbitest r-cran-gert r-cran-gh r-cran-dichromat r-cran-dt 81s r-cran-formattable r-cran-pkgdown r-cran-zeallot r-cran-renv lmodern dvisvgm 81s picard-tools tabix gmap rna-star r-bioc-rots r-bioc-ctc r-cran-gplots 81s r-cran-ape libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl 81s x11-utils x11-xserver-utils 82s The following NEW packages will be installed: 82s adwaita-icon-theme at-spi2-common autopkgtest-satdep berkeley-express bowtie 82s bowtie2 ca-certificates-java dconf-gsettings-backend dconf-service 82s default-jre default-jre-headless fontconfig fontconfig-config 82s fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 82s fonts-glyphicons-halflings fonts-lmodern fonts-mathjax gtk-update-icon-cache 82s hicolor-icon-theme hisat2 humanity-icon-theme jaligner java-common 82s javascript-common jellyfish kallisto libapache-pom-java libasan8 82s libasound2-data libasound2t64 libatinject-jsr330-api-java 82s libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 libavahi-client3 82s libavahi-common-data libavahi-common3 libbamtools2.5.2 libbarclay-java 82s libbibtex-parser-perl libblas3 libboost-dev libboost-filesystem1.83.0 82s libboost-iostreams1.83.0 libboost-program-options1.83.0 82s libboost-thread1.83.0 libboost1.83-dev libcairo-gobject2 libcairo2 82s libclone-perl libcolord2 libcommons-codec-java libcommons-compress-java 82s libcommons-io-java libcommons-jexl2-java libcommons-lang3-java 82s libcommons-logging-java libcommons-math3-java libcommons-parent-java 82s libcups2t64 libdatrie1 libdconf1 libdeflate0 libdrm-amdgpu1 libdrm-intel1 82s libdrm-radeon1 libencode-locale-perl libepoxy0 liberror-prone-java 82s libfile-listing-perl libfontconfig1 libfreemarker-java 82s libgatk-native-bindings-java libgbm1 libgcc-14-dev libgdk-pixbuf-2.0-0 82s libgdk-pixbuf2.0-common libgetopt-java libgfortran5 libgif7 libgkl-java 82s libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 82s libgoogle-gson-java libgraphite2-3 libgtk-3-0t64 libgtk-3-common 82s libguava-java libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl 82s libhtml-tree-perl libhts3t64 libhtscodecs2 libhtsjdk-java 82s libhttp-cookies-perl libhttp-date-perl libhttp-message-perl 82s libhttp-negotiate-perl libhttpclient-java libhttpcore-java libhwasan0 82s libhwloc15 libice6 libio-html-perl libio-socket-ssl-perl libio-string-perl 82s libitm1 libjbig0 libjbzip2-java libjellyfish-2.0-2 libjemalloc2 82s libjoptsimple-java libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootstrap4 82s libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery 82s libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json 82s libjs-lunr libjs-mathjax libjs-microplugin.js libjs-modernizr 82s libjs-popper.js libjs-prettify libjs-sifter.js libjs-sphinxdoc 82s libjs-twitter-bootstrap-datepicker libjs-underscore libjsr305-java 82s libjung-free-java libkpathsea6 liblapack3 liblatex-tounicode-perl liblcms2-2 82s liblerc4 liblightcouch-java liblog4j2-java liblsan0 liblua5.4-0 82s liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto7t64 82s libmbedtls14t64 libmbedx509-1t64 libmjson-java libmongodb-java libmpfi0 82s libncbi-ngs3 libncbi-vdb3 libnet-http-perl libnet-ssleay-perl libngs-java 82s libngs-jni libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 82s libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libpicard-java 82s libpixman-1-0 libpotrace0 libprotobuf32t64 libptexenc1 libquadmath0 82s librhino-java libsharpyuv0 libslf4j-java libsm6 libsnappy-java libsnappy-jni 82s libsnappy1v5 libstaden-read14t64 libstdc++-14-dev libsynctex2 libtbb12 82s libtbbbind-2-5 libtbbmalloc2 libtcl8.6 libteckit0 libtexlua53-5 libthai-data 82s libthai0 libtiff6 libtimedate-perl libtk8.6 libtry-tiny-perl libtsan2 82s libubsan1 liburi-perl libvulkan1 libwayland-client0 libwayland-cursor0 82s libwayland-egl1 libwayland-server0 libwebp7 libwww-perl 82s libwww-robotrules-perl libx11-xcb1 libxaw7 libxcb-dri2-0 libxcb-dri3-0 82s libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 82s libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxcursor1 libxdamage1 82s libxfixes3 libxft2 libxi6 libxinerama1 libxmu6 libxpm4 libxrandr2 82s libxrender1 libxshmfence1 libxss1 libxt6t64 libxtst6 libxxf86vm1 82s libzzip-0-13t64 littler mesa-libgallium ncbi-blast+ ncbi-data ncbi-vdb-data 82s node-bootstrap-sass node-html5shiv node-normalize.css openjdk-21-jre 82s openjdk-21-jre-headless pandoc pandoc-data parafly perl-openssl-defaults 82s python3-hisat2 python3-htseq python3-numpy python3-pysam r-base-core 82s r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache 82s r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biocstyle 82s r-bioc-biocversion r-bioc-biomart r-bioc-biostrings r-bioc-delayedarray 82s r-bioc-deseq2 r-bioc-dexseq r-bioc-edger r-bioc-genefilter 82s r-bioc-genelendatabase r-bioc-geneplotter r-bioc-genomeinfodb 82s r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures 82s r-bioc-genomicranges r-bioc-go.db r-bioc-goseq r-bioc-iranges 82s r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics r-bioc-qvalue 82s r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays 82s r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment 82s r-bioc-txdbmaker r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc 82s r-cran-abind r-cran-argparse r-cran-askpass r-cran-backports 82s r-cran-base64enc r-cran-bh r-cran-biasedurn r-cran-biocmanager r-cran-bit 82s r-cran-bit64 r-cran-bitops r-cran-blob r-cran-bookdown r-cran-broom 82s r-cran-bslib r-cran-cachem r-cran-callr r-cran-cellranger r-cran-cli 82s r-cran-clipr r-cran-cluster r-cran-codetools r-cran-colorspace 82s r-cran-commonmark r-cran-conflicted r-cran-cpp11 r-cran-crayon r-cran-curl 82s r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr 82s r-cran-dtplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver 82s r-cran-fastcluster r-cran-fastmap r-cran-filelock r-cran-findpython 82s r-cran-fontawesome r-cran-forcats r-cran-formatr r-cran-fs 82s r-cran-futile.logger r-cran-futile.options r-cran-gargle r-cran-generics 82s r-cran-ggdendro r-cran-ggplot2 r-cran-glue r-cran-googledrive 82s r-cran-googlesheets4 r-cran-goplot r-cran-gridextra r-cran-gtable 82s r-cran-haven r-cran-highr r-cran-hms r-cran-htmltools r-cran-httpuv 82s r-cran-httr r-cran-httr2 r-cran-hwriter r-cran-ids r-cran-isoband 82s r-cran-jquerylib r-cran-jsonlite r-cran-kernsmooth r-cran-knitr 82s r-cran-labeling r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lifecycle 82s r-cran-littler r-cran-locfit r-cran-lubridate r-cran-magrittr r-cran-mass 82s r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime 82s r-cran-modelr r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar 82s r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-plyr r-cran-png 82s r-cran-prettyunits r-cran-processx r-cran-progress r-cran-promises r-cran-ps 82s r-cran-purrr r-cran-r6 r-cran-ragg r-cran-rappdirs r-cran-rcolorbrewer 82s r-cran-rcpp r-cran-rcpparmadillo r-cran-rcurl r-cran-readr r-cran-readxl 82s r-cran-rematch r-cran-rematch2 r-cran-reprex r-cran-reshape2 r-cran-restfulr 82s r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-rstudioapi 82s r-cran-rvest r-cran-sass r-cran-scales r-cran-selectr r-cran-shiny 82s r-cran-snow r-cran-sourcetools r-cran-statmod r-cran-stringi r-cran-stringr 82s r-cran-survival r-cran-sys r-cran-systemfonts r-cran-textshaping 82s r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tidyverse 82s r-cran-timechange r-cran-tinytex r-cran-tzdb r-cran-utf8 r-cran-uuid 82s r-cran-vctrs r-cran-viridislite r-cran-vroom r-cran-withr r-cran-xfun 82s r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml rsem salmon samtools 82s subread t1utils tex-common texlive-base texlive-bibtex-extra 82s texlive-binaries texlive-latex-base trimmomatic trinityrnaseq 82s trinityrnaseq-examples ubuntu-mono unzip x11-common xdg-utils zip zlib1g-dev 82s 0 upgraded, 474 newly installed, 0 to remove and 0 not upgraded. 82s Need to get 989 MB/989 MB of archives. 82s After this operation, 2397 MB of additional disk space will be used. 82s Get:1 /tmp/autopkgtest.zV67tP/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [828 B] 82s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [7888 B] 82s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 82s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 82s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.21-1 [49.8 kB] 82s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 82s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 82s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 82s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 82s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 82s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1 [147 kB] 82s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 gtk-update-icon-cache amd64 4.16.2+ds-2 [51.1 kB] 82s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 hicolor-icon-theme all 0.18-1 [13.5 kB] 82s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 humanity-icon-theme all 0.6.16 [1282 kB] 82s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-mono all 24.04-0ubuntu1 [151 kB] 82s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 adwaita-icon-theme all 47.0-1 [525 kB] 82s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 at-spi2-common all 2.54.0-1 [8774 B] 82s Get:18 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6 [141 kB] 82s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-3.2ubuntu2 [286 kB] 82s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-program-options1.83.0 amd64 1.83.0-3.2ubuntu2 [322 kB] 82s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-thread1.83.0 amd64 1.83.0-3.2ubuntu2 [278 kB] 82s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libprotobuf32t64 amd64 3.21.12-9ubuntu1 [941 kB] 82s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 berkeley-express amd64 1.5.3+dfsg-3build5 [210 kB] 82s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 ca-certificates-java all 20240118 [11.6 kB] 82s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libdconf1 amd64 0.40.0-4build2 [39.4 kB] 82s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-service amd64 0.40.0-4build2 [27.5 kB] 82s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-gsettings-backend amd64 0.40.0-4build2 [22.1 kB] 82s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 java-common all 0.76 [6852 B] 82s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.14-2build1 [161 kB] 82s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcsclite1 amd64 2.3.0-1 [23.9 kB] 82s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 openjdk-21-jre-headless amd64 21.0.5+11-1 [46.4 MB] 83s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 default-jre-headless amd64 2:1.21-76 [3178 B] 83s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libatk1.0-0t64 amd64 2.54.0-1 [55.1 kB] 83s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB] 83s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libatspi2.0-0t64 amd64 2.54.0-1 [79.6 kB] 83s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libatk-bridge2.0-0t64 amd64 2.54.0-1 [66.3 kB] 83s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 83s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 83s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 83s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 83s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.42.2-1build1 [279 kB] 83s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 83s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 83s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 83s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 83s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo-gobject2 amd64 1.18.2-2 [127 kB] 83s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libcolord2 amd64 1.4.7-1build2 [149 kB] 83s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common-data amd64 0.8-13ubuntu6 [29.7 kB] 83s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common3 amd64 0.8-13ubuntu6 [23.3 kB] 83s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-client3 amd64 0.8-13ubuntu6 [26.8 kB] 83s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libcups2t64 amd64 2.4.10-1ubuntu2 [271 kB] 83s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libepoxy0 amd64 1.5.10-1build1 [220 kB] 83s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 83s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 9.0.0-1 [487 kB] 83s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB] 83s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 83s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 83s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 83s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.54.0+ds-2 [235 kB] 83s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-2 [49.1 kB] 83s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-2 [28.8 kB] 83s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-client0 amd64 1.23.0-1 [27.1 kB] 83s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-cursor0 amd64 1.23.0-1 [10.8 kB] 83s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-egl1 amd64 1.23.0-1 [5662 B] 83s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcomposite1 amd64 1:0.4.5-1build3 [6320 B] 83s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libxfixes3 amd64 1:6.0.0-2build1 [10.8 kB] 83s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcursor1 amd64 1:1.2.2-1 [20.9 kB] 83s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libxdamage1 amd64 1:1.1.6-1build1 [6150 B] 83s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libxinerama1 amd64 2:1.1.4-3build1 [6396 B] 83s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrandr2 amd64 2:1.5.4-1 [19.6 kB] 83s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-3-common all 3.24.43-3ubuntu2 [1202 kB] 83s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-3-0t64 amd64 3.24.43-3ubuntu2 [2927 kB] 83s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libglvnd0 amd64 1.7.0-1build1 [69.6 kB] 83s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libglapi-mesa amd64 24.2.3-1ubuntu1 [42.4 kB] 83s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libx11-xcb1 amd64 2:1.8.7-1build1 [7800 B] 83s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-dri2-0 amd64 1.17.0-2 [7222 B] 83s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-dri3-0 amd64 1.17.0-2 [7508 B] 83s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-glx0 amd64 1.17.0-2 [24.8 kB] 83s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-present0 amd64 1.17.0-2 [6064 B] 83s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-randr0 amd64 1.17.0-2 [17.9 kB] 83s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-sync1 amd64 1.17.0-2 [9312 B] 83s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xfixes0 amd64 1.17.0-2 [10.2 kB] 83s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libxshmfence1 amd64 1.3-1build5 [4764 B] 83s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libxxf86vm1 amd64 1:1.1.4-1build4 [9282 B] 83s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-amdgpu1 amd64 2.4.122-1 [20.9 kB] 83s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 83s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-intel1 amd64 2.4.122-1 [64.6 kB] 83s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-radeon1 amd64 2.4.122-1 [21.0 kB] 83s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 mesa-libgallium amd64 24.2.3-1ubuntu1 [9904 kB] 83s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 libvulkan1 amd64 1.3.290.0-1 [143 kB] 83s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-server0 amd64 1.23.0-1 [35.1 kB] 83s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libgbm1 amd64 24.2.3-1ubuntu1 [32.0 kB] 83s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 libgl1-mesa-dri amd64 24.2.3-1ubuntu1 [34.4 kB] 83s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 libglx-mesa0 amd64 24.2.3-1ubuntu1 [153 kB] 83s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 libglx0 amd64 1.7.0-1build1 [38.6 kB] 83s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 libgl1 amd64 1.7.0-1build1 [102 kB] 83s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 libasound2-data all 1.2.12-1 [21.0 kB] 83s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 libasound2t64 amd64 1.2.12-1 [394 kB] 83s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 libgif7 amd64 5.2.2-1ubuntu1 [35.2 kB] 83s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 83s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 libxtst6 amd64 2:1.2.3-1.1build1 [12.6 kB] 83s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 openjdk-21-jre amd64 21.0.5+11-1 [220 kB] 83s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 default-jre amd64 2:1.21-76 [918 B] 83s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 83s Get:105 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 83s Get:106 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lmodern all 2.005-1 [4799 kB] 83s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 83s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 hisat2 amd64 2.2.1-5 [3889 kB] 83s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 jaligner all 1.0+dfsg-11 [136 kB] 83s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 javascript-common all 11+nmu1 [5936 B] 83s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.0-1build1 [98.8 kB] 83s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 83s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjellyfish-2.0-2 amd64 2.3.1-3build2 [69.3 kB] 83s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 jellyfish amd64 2.3.1-3build2 [772 kB] 83s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 kallisto amd64 0.48.0+dfsg-4build1 [273 kB] 83s Get:116 http://ftpmaster.internal/ubuntu plucky/universe amd64 libapache-pom-java all 33-2 [5874 B] 83s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-7ubuntu1 [2998 kB] 83s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5348 B] 83s Get:119 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-parent-java all 56-1 [10.7 kB] 83s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-lang3-java all 3.14.0-1 [586 kB] 83s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfreemarker-java all 2.3.32-2 [1542 kB] 83s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgoogle-gson-java all 2.10.1-1 [252 kB] 83s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjoptsimple-java all 5.0.4-4 [73.1 kB] 83s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-codec-java all 1.16.0-1 [306 kB] 83s Get:125 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 83s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhttpcore-java all 4.4.16-1 [612 kB] 83s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhttpclient-java all 4.5.14-1 [1241 kB] 83s Get:128 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblightcouch-java all 0.2.0-1 [74.2 kB] 83s Get:129 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmongodb-java all 3.6.3-2 [1899 kB] 83s Get:130 http://ftpmaster.internal/ubuntu plucky/universe amd64 libslf4j-java all 1.7.32-1 [141 kB] 83s Get:131 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblog4j2-java all 2.19.0-2 [2294 kB] 83s Get:132 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbarclay-java all 5.0.0+dfsg-1 [108 kB] 83s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 libio-string-perl all 1.08-4 [11.1 kB] 83s Get:134 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblatex-tounicode-perl all 0.54-2 [29.0 kB] 83s Get:135 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbibtex-parser-perl all 1.04+dfsg-1 [16.7 kB] 83s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 83s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-7ubuntu1 [148 kB] 83s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-7ubuntu1 [29.1 kB] 83s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-7ubuntu1 [1316 kB] 83s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-7ubuntu1 [2733 kB] 83s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-7ubuntu1 [1177 kB] 83s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-7ubuntu1 [1634 kB] 83s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-7ubuntu1 [153 kB] 83s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-7ubuntu1 [2814 kB] 83s Get:145 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-7ubuntu1 [2503 kB] 83s Get:146 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost1.83-dev amd64 1.83.0-3.2ubuntu2 [10.7 MB] 83s Get:147 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-dev amd64 1.83.0.2ubuntu1 [4468 B] 83s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-3.2ubuntu2 [260 kB] 83s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 libclone-perl amd64 0.47-1 [10.7 kB] 83s Get:150 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-compress-java all 1.25.0-1 [612 kB] 83s Get:151 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-io-java all 2.16.1-1 [451 kB] 83s Get:152 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-jexl2-java all 2.1.1-6 [250 kB] 83s Get:153 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-math3-java all 3.6.1-3 [2016 kB] 83s Get:154 http://ftpmaster.internal/ubuntu plucky/main amd64 libencode-locale-perl all 1.05-3 [11.6 kB] 83s Get:155 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjsr305-java all 0.1~+svn49-11 [27.0 kB] 83s Get:156 http://ftpmaster.internal/ubuntu plucky/universe amd64 libguava-java all 32.0.1-1 [2692 kB] 83s Get:157 http://ftpmaster.internal/ubuntu plucky/universe amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] 83s Get:158 http://ftpmaster.internal/ubuntu plucky/main amd64 libtimedate-perl all 2.3300-2 [34.0 kB] 83s Get:159 http://ftpmaster.internal/ubuntu plucky/main amd64 libhttp-date-perl all 6.06-1 [10.2 kB] 83s Get:160 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-listing-perl all 6.16-1 [11.3 kB] 83s Get:161 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8014 B] 83s Get:162 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgetopt-java all 1.0.14+dfsg-6 [23.0 kB] 83s Get:163 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-7ubuntu1 [909 kB] 83s Get:164 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmjson-java all 1.4.0-3 [60.4 kB] 83s Get:165 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedcrypto7t64 amd64 2.28.8-1 [209 kB] 83s Get:166 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedx509-1t64 amd64 2.28.8-1 [46.6 kB] 83s Get:167 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedtls14t64 amd64 2.28.8-1 [82.2 kB] 83s Get:168 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-vdb-data all 3.0.2+dfsg-2build2 [67.5 kB] 83s Get:169 http://ftpmaster.internal/ubuntu plucky/universe amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2build2 [1112 kB] 83s Get:170 http://ftpmaster.internal/ubuntu plucky/universe amd64 libncbi-ngs3 amd64 3.0.3+dfsg-9ubuntu1 [149 kB] 83s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 libngs-jni amd64 3.0.3+dfsg-9ubuntu1 [4848 B] 83s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 libngs-java amd64 3.0.3+dfsg-9ubuntu1 [91.1 kB] 83s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 librhino-java all 1.7.14-2.1 [1330 kB] 83s Get:174 http://ftpmaster.internal/ubuntu plucky/main amd64 libsnappy1v5 amd64 1.2.1-1 [30.4 kB] 83s Get:175 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsnappy-jni amd64 1.1.10.5-2 [6622 B] 83s Get:176 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsnappy-java all 1.1.10.5-2 [83.7 kB] 83s Get:177 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtsjdk-java all 4.1.0+dfsg-2 [1823 kB] 83s Get:178 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgkl-java all 0.8.11+dfsg-2build1 [24.9 kB] 83s Get:179 http://ftpmaster.internal/ubuntu plucky/main amd64 libhtml-tagset-perl all 3.24-1 [14.1 kB] 83s Get:180 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 liburi-perl all 5.30-1 [94.4 kB] 83s Get:181 http://ftpmaster.internal/ubuntu plucky/main amd64 libhtml-parser-perl amd64 3.83-1build1 [86.2 kB] 83s Get:182 http://ftpmaster.internal/ubuntu plucky/main amd64 libhtml-tree-perl all 5.07-3 [200 kB] 83s Get:183 http://ftpmaster.internal/ubuntu plucky/main amd64 libio-html-perl all 1.004-3 [15.9 kB] 83s Get:184 http://ftpmaster.internal/ubuntu plucky/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.1 kB] 83s Get:185 http://ftpmaster.internal/ubuntu plucky/main amd64 libhttp-message-perl all 6.46-1ubuntu1 [75.9 kB] 83s Get:186 http://ftpmaster.internal/ubuntu plucky/main amd64 libhttp-cookies-perl all 6.11-1 [18.2 kB] 83s Get:187 http://ftpmaster.internal/ubuntu plucky/main amd64 libhttp-negotiate-perl all 6.01-2 [12.4 kB] 83s Get:188 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc15 amd64 2.11.0-2 [173 kB] 83s Get:189 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.0.10-1build3 [41.4 kB] 83s Get:190 http://ftpmaster.internal/ubuntu plucky/main amd64 perl-openssl-defaults amd64 7build3 [6626 B] 83s Get:191 http://ftpmaster.internal/ubuntu plucky/main amd64 libnet-ssleay-perl amd64 1.94-2 [317 kB] 83s Get:192 http://ftpmaster.internal/ubuntu plucky/main amd64 libio-socket-ssl-perl all 2.088-1 [200 kB] 83s Get:193 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjemalloc2 amd64 5.3.0-2build1 [256 kB] 83s Get:194 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 83s Get:195 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-popper.js all 1.16.1+ds-6 [54.1 kB] 83s Get:196 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [537 kB] 83s Get:197 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-d3 all 3.5.17-4 [132 kB] 83s Get:198 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-es5-shim all 4.6.7-2 [39.8 kB] 83s Get:199 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 83s Get:200 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 83s Get:201 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 83s Get:202 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB] 83s Get:203 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3712 B] 83s Get:204 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB] 83s Get:205 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 83s Get:206 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-json all 0~20221030+~1.0.8-1 [20.6 kB] 83s Get:207 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-lunr all 2.3.9~dfsg-2 [66.8 kB] 83s Get:208 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-prettify all 2015.12.04+dfsg-1.1 [39.3 kB] 83s Get:209 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 83s Get:210 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-3 [157 kB] 83s Get:211 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjung-free-java all 2.1.1-2 [1471 kB] 83s Get:212 http://ftpmaster.internal/ubuntu plucky/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-4 [64.3 kB] 83s Get:213 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 83s Get:214 http://ftpmaster.internal/ubuntu plucky/main amd64 liblua5.4-0 amd64 5.4.6-3build2 [166 kB] 83s Get:215 http://ftpmaster.internal/ubuntu plucky/main amd64 libnet-http-perl all 6.23-1 [22.3 kB] 83s Get:216 http://ftpmaster.internal/ubuntu plucky/main amd64 libtry-tiny-perl all 0.31-2 [20.8 kB] 83s Get:217 http://ftpmaster.internal/ubuntu plucky/main amd64 libwww-robotrules-perl all 6.02-1 [12.6 kB] 83s Get:218 http://ftpmaster.internal/ubuntu plucky/main amd64 libwww-perl all 6.77-1 [138 kB] 83s Get:219 http://ftpmaster.internal/ubuntu plucky/main amd64 liblwp-protocol-https-perl all 6.14-1 [9040 B] 83s Get:220 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmpfi0 amd64 1.5.4+ds-3 [35.1 kB] 83s Get:221 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper1 amd64 1.1.29build1 [13.4 kB] 83s Get:222 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 1.1.29build1 [8650 B] 83s Get:223 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpicard-java all 3.1.1+dfsg-1 [1731 kB] 84s Get:224 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpotrace0 amd64 1.16-2build1 [17.7 kB] 84s Get:225 http://ftpmaster.internal/ubuntu plucky/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-4 [41.9 kB] 84s Get:226 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.3-1build3 [15.7 kB] 84s Get:227 http://ftpmaster.internal/ubuntu plucky/universe amd64 libstaden-read14t64 amd64 1.15.0-1.1build2 [251 kB] 84s Get:228 http://ftpmaster.internal/ubuntu plucky/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-4 [59.9 kB] 84s Get:229 http://ftpmaster.internal/ubuntu plucky/universe amd64 libtbbmalloc2 amd64 2021.12.0-1ubuntu2 [52.5 kB] 84s Get:230 http://ftpmaster.internal/ubuntu plucky/universe amd64 libtbbbind-2-5 amd64 2021.12.0-1ubuntu2 [15.4 kB] 84s Get:231 http://ftpmaster.internal/ubuntu plucky/universe amd64 libtbb12 amd64 2021.12.0-1ubuntu2 [89.3 kB] 84s Get:232 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1build1 [988 kB] 84s Get:233 http://ftpmaster.internal/ubuntu plucky/universe amd64 libteckit0 amd64 2.5.12+ds1-1 [411 kB] 84s Get:234 http://ftpmaster.internal/ubuntu plucky/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-4 [123 kB] 84s Get:235 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 84s Get:236 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 84s Get:237 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.14-1build1 [779 kB] 84s Get:238 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 84s Get:239 http://ftpmaster.internal/ubuntu plucky/main amd64 libxmu6 amd64 2:1.1.3-3build2 [47.6 kB] 84s Get:240 http://ftpmaster.internal/ubuntu plucky/main amd64 libxpm4 amd64 1:3.5.17-1build2 [36.5 kB] 84s Get:241 http://ftpmaster.internal/ubuntu plucky/main amd64 libxaw7 amd64 2:1.0.14-1build2 [187 kB] 84s Get:242 http://ftpmaster.internal/ubuntu plucky/universe amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.2build1 [28.1 kB] 84s Get:243 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14 [174 kB] 84s Get:244 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 84s Get:245 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 84s Get:246 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.1-1 [28.5 MB] 84s Get:247 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-littler amd64 0.3.20-1 [96.0 kB] 84s Get:248 http://ftpmaster.internal/ubuntu plucky/universe amd64 littler all 0.3.20-1 [2486 B] 84s Get:249 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-data all 6.1.20170106+dfsg2-3 [3966 kB] 84s Get:250 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-blast+ amd64 2.16.0+ds-6 [15.2 MB] 84s Get:251 http://ftpmaster.internal/ubuntu plucky/universe amd64 node-bootstrap-sass all 3.4.3-2 [187 kB] 84s Get:252 http://ftpmaster.internal/ubuntu plucky/universe amd64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 84s Get:253 http://ftpmaster.internal/ubuntu plucky/universe amd64 node-normalize.css all 8.0.1-5 [10.8 kB] 84s Get:254 http://ftpmaster.internal/ubuntu plucky/universe amd64 pandoc-data all 3.1.11.1-3 [78.7 kB] 84s Get:255 http://ftpmaster.internal/ubuntu plucky/universe amd64 pandoc amd64 3.1.11.1+ds-2 [27.2 MB] 84s Get:256 http://ftpmaster.internal/ubuntu plucky/universe amd64 parafly amd64 0.1.0-4 [16.5 kB] 84s Get:257 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-hisat2 all 2.2.1-5 [12.7 kB] 84s Get:258 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 84s Get:259 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB] 84s Get:260 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-htseq amd64 2.0.5-2 [319 kB] 84s Get:261 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocgenerics all 0.50.0-2 [605 kB] 84s Get:262 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biobase amd64 2.64.0-4 [2154 kB] 84s Get:263 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-s4vectors amd64 0.42.1+dfsg-2 [1890 kB] 84s Get:264 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-iranges amd64 2.38.1-1 [2298 kB] 84s Get:265 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dbi all 1.2.3-1 [853 kB] 84s Get:266 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bit amd64 4.0.5-1 [1063 kB] 84s Get:267 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bit64 amd64 4.0.5-1 [465 kB] 84s Get:268 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rlang amd64 1.1.4-1 [1708 kB] 84s Get:269 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cli amd64 3.6.2-1 [1380 kB] 84s Get:270 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-glue amd64 1.7.0-1 [154 kB] 84s Get:271 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 84s Get:272 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 84s Get:273 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-blob all 1.2.4-1 [49.8 kB] 84s Get:274 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fastmap amd64 1.1.1-1 [70.5 kB] 84s Get:275 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cachem amd64 1.0.8-1 [72.1 kB] 84s Get:276 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-memoise all 2.0.1-1 [53.9 kB] 84s Get:277 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 84s Get:278 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-plogr all 0.2.0-3build1 [15.1 kB] 84s Get:279 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cpp11 all 0.4.7-1 [266 kB] 84s Get:280 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rsqlite amd64 2.3.7-2 [1237 kB] 84s Get:281 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-curl amd64 5.2.1+dfsg-1 [180 kB] 84s Get:282 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-jsonlite amd64 1.8.8+dfsg-1 [441 kB] 84s Get:283 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mime amd64 0.12-2 [35.8 kB] 84s Get:284 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-sys amd64 3.4.2-1 [44.6 kB] 84s Get:285 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-askpass amd64 1.2.0-1 [24.6 kB] 84s Get:286 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-openssl amd64 2.2.0+dfsg-1 [405 kB] 84s Get:287 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r6 all 2.5.1-1 [99.0 kB] 84s Get:288 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] 84s Get:289 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-png amd64 0.1-8-1build2 [40.6 kB] 84s Get:290 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 84s Get:291 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-zlibbioc all 1.50.0+dfsg-2 [10.1 kB] 84s Get:292 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-xvector amd64 0.44.0-1 [624 kB] 84s Get:293 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-ucsc.utils all 1.0.0+ds-2 [77.0 kB] 84s Get:294 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomeinfodbdata all 1.2.12-1 [12.6 MB] 85s Get:295 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomeinfodb all 1.40.1+dfsg-1 [3883 kB] 85s Get:296 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-crayon all 1.5.2-1 [164 kB] 85s Get:297 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biostrings amd64 2.72.1+dfsg-1 [13.2 MB] 85s Get:298 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-keggrest all 1.44.1+dfsg-1 [188 kB] 85s Get:299 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-annotationdbi all 1.66.0-1 [4848 kB] 85s Get:300 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xml amd64 3.99-0.17-1 [1745 kB] 85s Get:301 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xtable all 1:1.8-4-2 [689 kB] 85s Get:302 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-annotate all 1.82.0+dfsg-1 [1765 kB] 85s Get:303 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-generics all 0.1.3-1 [81.3 kB] 85s Get:304 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 85s Get:305 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fansi amd64 1.0.5-1 [619 kB] 85s Get:306 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB] 85s Get:307 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 85s Get:308 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [415 kB] 85s Get:309 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-withr all 3.0.0+dfsg-1 [228 kB] 85s Get:310 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [222 kB] 85s Get:311 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dplyr amd64 1.1.4-1 [1515 kB] 85s Get:312 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-purrr amd64 1.0.2-1 [502 kB] 85s Get:313 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-stringi amd64 1.8.3-1 [873 kB] 85s Get:314 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB] 85s Get:315 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB] 85s Get:316 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dbplyr all 2.4.0+dfsg-1 [1172 kB] 85s Get:317 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-filelock amd64 1.0.3-1 [29.6 kB] 85s Get:318 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocfilecache all 2.12.0+dfsg-1 [304 kB] 85s Get:319 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocio all 1.14.0+dfsg-1 [215 kB] 85s Get:320 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-formatr all 1.14-2 [152 kB] 85s Get:321 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lambda.r all 1.2.4-2build1 [119 kB] 85s Get:322 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-futile.options all 1.0.1-3build1 [20.2 kB] 85s Get:323 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-futile.logger all 1.4.3-4build1 [99.3 kB] 85s Get:324 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-snow all 1:0.4.4-2 [97.6 kB] 85s Get:325 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-codetools all 0.2-20-1 [90.5 kB] 85s Get:326 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bh all 1.84.0-1 [5962 B] 85s Get:327 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocparallel amd64 1.38.0-2 [1342 kB] 85s Get:328 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-base64enc amd64 0.1-3-3 [27.6 kB] 85s Get:329 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-digest amd64 0.6.36-1 [199 kB] 85s Get:330 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-htmltools amd64 0.5.8.1-1 [373 kB] 85s Get:331 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-evaluate all 0.24.0-1 [93.5 kB] 85s Get:332 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xfun amd64 0.45+dfsg-1 [518 kB] 85s Get:333 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 85s Get:334 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-yaml amd64 2.3.8-2 [108 kB] 85s Get:335 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 85s Get:336 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-knitr all 1.47+dfsg-1 [911 kB] 85s Get:337 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.5 kB] 85s Get:338 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fs amd64 1.6.4+dfsg-1 [245 kB] 85s Get:339 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rappdirs amd64 0.3.3-1 [47.5 kB] 85s Get:340 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-sass amd64 0.4.9+dfsg-1 [1001 kB] 85s Get:341 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bslib all 0.7.0+dfsg-1 [4255 kB] 85s Get:342 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fontawesome all 0.5.2-1 [1300 kB] 85s Get:343 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tinytex all 0.51-1 [145 kB] 85s Get:344 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-modernizr all 3.13.0-0.1 [101 kB] 85s Get:345 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 85s Get:346 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcpp amd64 1.0.13-1 [1990 kB] 85s Get:347 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-later amd64 1.3.2+dfsg-1 [123 kB] 85s Get:348 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-promises amd64 1.3.0+dfsg-1 [287 kB] 85s Get:349 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [510 kB] 85s Get:350 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-sourcetools amd64 0.1.7-1-1 [48.1 kB] 85s Get:351 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-commonmark amd64 1.9.1-1 [131 kB] 85s Get:352 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB] 85s Get:353 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-shiny all 1.8.1.1+dfsg-1 [2873 kB] 85s Get:354 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rmarkdown all 2.27+dfsg-1 [1501 kB] 85s Get:355 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bookdown all 0.40+dfsg-1 [1409 kB] 85s Get:356 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-biocmanager all 1.30.22+dfsg-2 [125 kB] 85s Get:357 http://ftpmaster.internal/ubuntu plucky/universe amd64 tex-common all 6.18 [32.8 kB] 85s Get:358 http://ftpmaster.internal/ubuntu plucky/main amd64 t1utils amd64 1.41-4build3 [61.3 kB] 85s Get:359 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-binaries amd64 2024.20240313.70630+ds-4 [8478 kB] 85s Get:360 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-base all 2024.20240706-1 [22.5 MB] 86s Get:361 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-latex-base all 2024.20240706-1 [1256 kB] 86s Get:362 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-bibtex-extra all 2024.20240706-2 [79.1 MB] 87s Get:363 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocversion all 3.19.1-1 [11.2 kB] 87s Get:364 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocstyle all 2.32.1+dfsg-1 [452 kB] 87s Get:365 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-hms all 1.1.3-1 [96.5 kB] 87s Get:366 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-prettyunits all 1.2.0-1 [162 kB] 87s Get:367 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-progress all 1.2.3-1 [91.9 kB] 87s Get:368 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-httr2 all 1.0.2-1 [571 kB] 87s Get:369 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xml2 amd64 1.3.6-1 [322 kB] 87s Get:370 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biomart all 2.60.1+dfsg-1 [431 kB] 87s Get:371 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB] 87s Get:372 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrix amd64 1.7-0-3 [4185 kB] 87s Get:373 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrixstats amd64 1.3.0-1 [505 kB] 87s Get:374 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-matrixgenerics all 1.16.0-2 [424 kB] 87s Get:375 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-abind all 1.4-5-2 [63.6 kB] 87s Get:376 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-s4arrays amd64 1.4.1+dfsg-1 [525 kB] 87s Get:377 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-sparsearray amd64 1.4.8+dfsg-1 [1254 kB] 87s Get:378 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-delayedarray amd64 0.30.1+dfsg-1 [1846 kB] 87s Get:379 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomicranges amd64 1.56.1+dfsg-1 [1840 kB] 87s Get:380 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-summarizedexperiment all 1.34.0+dfsg-1 [1134 kB] 87s Get:381 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-locfit amd64 1.5-9.9-1 [518 kB] 87s Get:382 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-gtable all 0.3.5+dfsg-1 [192 kB] 87s Get:383 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 87s Get:384 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mass amd64 7.3-61-1 [1109 kB] 87s Get:385 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nlme amd64 3.1.166-1 [2314 kB] 87s Get:386 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB] 87s Get:387 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB] 87s Get:388 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 87s Get:389 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1541 kB] 87s Get:390 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-munsell all 0.5.1-1 [213 kB] 87s Get:391 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 87s Get:392 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-viridislite all 0.4.2-2 [1088 kB] 87s Get:393 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-scales all 1.3.0-1 [603 kB] 87s Get:394 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 87s Get:395 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcpparmadillo amd64 14.0.0-1-1 [866 kB] 87s Get:396 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-deseq2 amd64 1.44.0+dfsg-1 [1236 kB] 87s Get:397 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-hwriter all 1.3.2.1-1 [106 kB] 87s Get:398 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bitops amd64 1.0-7-1 [29.8 kB] 87s Get:399 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-rhtslib amd64 3.0.0+dfsg-1 [1413 kB] 87s Get:400 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-rsamtools amd64 2.20.0+dfsg-1 [3684 kB] 87s Get:401 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-statmod amd64 1.5.0-1 [295 kB] 87s Get:402 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-geneplotter all 1.82.0+dfsg-1 [1417 kB] 87s Get:403 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-survival amd64 3.7-0-1 [6271 kB] 87s Get:404 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genefilter amd64 1.86.0-1 [1113 kB] 87s Get:405 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-dexseq all 1.50.0+dfsg-1 [452 kB] 87s Get:406 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-limma amd64 3.60.4+dfsg-1 [1955 kB] 87s Get:407 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-edger amd64 4.2.1+dfsg-1 [1181 kB] 87s Get:408 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomicalignments amd64 1.40.0-1 [2149 kB] 87s Get:409 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcurl amd64 1.98-1.14+dfsg-1build2 [793 kB] 87s Get:410 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rjson amd64 0.2.21-1 [143 kB] 87s Get:411 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-restfulr amd64 0.0.15-1 [380 kB] 87s Get:412 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-rtracklayer amd64 1.64.0-1 [5074 kB] 87s Get:413 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomicfeatures all 1.56.0+dfsg-1 [980 kB] 87s Get:414 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-txdbmaker all 1.0.1+ds-1 [875 kB] 87s Get:415 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genelendatabase all 1.40.1-1 [100 MB] 88s Get:416 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-go.db all 3.19.1-1 [17.7 MB] 88s Get:417 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-biasedurn amd64 2.0.11-1 [279 kB] 88s Get:418 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-goseq all 1.56.0-1 [1754 kB] 88s Get:419 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] 88s Get:420 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-reshape2 amd64 1.4.4-2build1 [114 kB] 88s Get:421 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-qvalue all 2.36.0-1 [2805 kB] 88s Get:422 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-findpython all 1.0.8-1 [24.2 kB] 88s Get:423 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-argparse all 2.2.3+dfsg-1 [143 kB] 88s Get:424 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-backports amd64 1.5.0-2 [121 kB] 88s Get:425 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-broom all 1.0.6+dfsg-1 [1803 kB] 88s Get:426 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ps amd64 1.7.6-1 [313 kB] 88s Get:427 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-processx amd64 3.8.4-1 [353 kB] 88s Get:428 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-callr all 3.7.6-1 [458 kB] 88s Get:429 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rematch all 2.0.0-1 [18.3 kB] 88s Get:430 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cellranger all 1.1.0-3 [102 kB] 89s Get:431 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-clipr all 0.8.0-1 [53.5 kB] 89s Get:432 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cluster amd64 2.1.6-1build1 [553 kB] 89s Get:433 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-conflicted all 1.2.0-1.1 [60.8 kB] 89s Get:434 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-data.table amd64 1.15.4+dfsg-2.2 [1860 kB] 89s Get:435 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dtplyr all 1.3.1-1 [364 kB] 89s Get:436 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ellipsis amd64 0.3.2-2 [35.6 kB] 89s Get:437 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fastcluster amd64 1.2.6-1build1 [192 kB] 89s Get:438 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-forcats all 1.0.0-1 [369 kB] 89s Get:439 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-gargle all 1.5.2-1 [737 kB] 89s Get:440 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ggdendro all 0.2.0+dfsg-1 [173 kB] 89s Get:441 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-uuid amd64 1.2-1-1 [48.5 kB] 89s Get:442 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-googledrive all 2.1.1-1 [1224 kB] 89s Get:443 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ids all 1.0.1-2 [124 kB] 89s Get:444 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rematch2 all 2.1.2-2build1 [46.5 kB] 89s Get:445 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-googlesheets4 all 1.1.1-1 [520 kB] 89s Get:446 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-gridextra all 2.3-3build1 [1024 kB] 89s Get:447 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-goplot all 1.0.2-2 [2427 kB] 89s Get:448 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tzdb amd64 0.4.0-2 [521 kB] 89s Get:449 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-vroom amd64 1.6.5-1 [848 kB] 89s Get:450 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-readr amd64 2.1.5-1 [766 kB] 89s Get:451 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-haven amd64 2.5.4-1 [346 kB] 89s Get:452 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-kernsmooth amd64 2.23-24-1 [92.9 kB] 89s Get:453 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-timechange amd64 0.3.0-1 [178 kB] 89s Get:454 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lubridate amd64 1.9.3+dfsg-1 [1010 kB] 89s Get:455 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-modelr all 0.1.11-1 [195 kB] 89s Get:456 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-systemfonts amd64 1.1.0-1 [245 kB] 89s Get:457 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-textshaping amd64 0.3.7-2 [95.5 kB] 89s Get:458 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ragg amd64 1.3.2-1 [495 kB] 89s Get:459 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-readxl amd64 1.4.3-1 [736 kB] 89s Get:460 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rstudioapi all 0.16.0-1 [287 kB] 89s Get:461 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-reprex all 2.1.0-1 [465 kB] 89s Get:462 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-selectr all 0.4-2-2build1 [416 kB] 89s Get:463 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rvest all 1.0.4-1 [298 kB] 89s Get:464 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tidyverse all 2.0.0+dfsg-1 [84.5 kB] 89s Get:465 http://ftpmaster.internal/ubuntu plucky/universe amd64 bowtie amd64 1.3.1-3 [1562 kB] 89s Get:466 http://ftpmaster.internal/ubuntu plucky/universe amd64 bowtie2 amd64 2.5.4-1 [1336 kB] 89s Get:467 http://ftpmaster.internal/ubuntu plucky/universe amd64 rsem amd64 1.3.3+dfsg-3build1 [36.1 MB] 89s Get:468 http://ftpmaster.internal/ubuntu plucky/universe amd64 salmon amd64 1.10.2+ds1-1build2 [3308 kB] 89s Get:469 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.20-3 [599 kB] 89s Get:470 http://ftpmaster.internal/ubuntu plucky/universe amd64 subread amd64 2.0.6+dfsg-3 [613 kB] 89s Get:471 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjbzip2-java all 0.9.1-8 [42.4 kB] 89s Get:472 http://ftpmaster.internal/ubuntu plucky/universe amd64 trimmomatic all 0.39+dfsg-2 [758 kB] 89s Get:473 http://ftpmaster.internal/ubuntu plucky/universe amd64 trinityrnaseq amd64 2.15.1+dfsg-5build1 [1718 kB] 89s Get:474 http://ftpmaster.internal/ubuntu plucky/universe amd64 trinityrnaseq-examples amd64 2.15.1+dfsg-5build1 [299 MB] 93s Preconfiguring packages ... 93s Fetched 989 MB in 10s (99.5 MB/s) 93s Selecting previously unselected package libgdk-pixbuf2.0-common. 93s (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 ... 75323 files and directories currently installed.) 93s Preparing to unpack .../000-libgdk-pixbuf2.0-common_2.42.12+dfsg-1_all.deb ... 93s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... 93s Selecting previously unselected package libjpeg-turbo8:amd64. 93s Preparing to unpack .../001-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 93s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 93s Selecting previously unselected package libjpeg8:amd64. 93s Preparing to unpack .../002-libjpeg8_8c-2ubuntu11_amd64.deb ... 93s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 93s Selecting previously unselected package libdeflate0:amd64. 93s Preparing to unpack .../003-libdeflate0_1.21-1_amd64.deb ... 93s Unpacking libdeflate0:amd64 (1.21-1) ... 93s Selecting previously unselected package libjbig0:amd64. 93s Preparing to unpack .../004-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 93s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 94s Selecting previously unselected package liblerc4:amd64. 94s Preparing to unpack .../005-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 94s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 94s Selecting previously unselected package libsharpyuv0:amd64. 94s Preparing to unpack .../006-libsharpyuv0_1.4.0-0.1_amd64.deb ... 94s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 94s Selecting previously unselected package libwebp7:amd64. 94s Preparing to unpack .../007-libwebp7_1.4.0-0.1_amd64.deb ... 94s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 94s Selecting previously unselected package libtiff6:amd64. 94s Preparing to unpack .../008-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 94s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 94s Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. 94s Preparing to unpack .../009-libgdk-pixbuf-2.0-0_2.42.12+dfsg-1_amd64.deb ... 94s Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1) ... 94s Selecting previously unselected package gtk-update-icon-cache. 94s Preparing to unpack .../010-gtk-update-icon-cache_4.16.2+ds-2_amd64.deb ... 94s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 94s No diversion 'diversion of /usr/share/man/man8/update-icon-caches.8.gz to /usr/share/man/man8/update-icon-caches.gtk2.8.gz by libgtk-3-bin', none removed. 94s Unpacking gtk-update-icon-cache (4.16.2+ds-2) ... 94s Selecting previously unselected package hicolor-icon-theme. 94s Preparing to unpack .../011-hicolor-icon-theme_0.18-1_all.deb ... 94s Unpacking hicolor-icon-theme (0.18-1) ... 94s Selecting previously unselected package humanity-icon-theme. 94s Preparing to unpack .../012-humanity-icon-theme_0.6.16_all.deb ... 94s Unpacking humanity-icon-theme (0.6.16) ... 95s Selecting previously unselected package ubuntu-mono. 95s Preparing to unpack .../013-ubuntu-mono_24.04-0ubuntu1_all.deb ... 95s Unpacking ubuntu-mono (24.04-0ubuntu1) ... 95s Selecting previously unselected package adwaita-icon-theme. 95s Preparing to unpack .../014-adwaita-icon-theme_47.0-1_all.deb ... 95s Unpacking adwaita-icon-theme (47.0-1) ... 96s Selecting previously unselected package at-spi2-common. 96s Preparing to unpack .../015-at-spi2-common_2.54.0-1_all.deb ... 96s Unpacking at-spi2-common (2.54.0-1) ... 96s Selecting previously unselected package libbamtools2.5.2:amd64. 96s Preparing to unpack .../016-libbamtools2.5.2_2.5.2+dfsg-6_amd64.deb ... 96s Unpacking libbamtools2.5.2:amd64 (2.5.2+dfsg-6) ... 96s Selecting previously unselected package libboost-filesystem1.83.0:amd64. 96s Preparing to unpack .../017-libboost-filesystem1.83.0_1.83.0-3.2ubuntu2_amd64.deb ... 96s Unpacking libboost-filesystem1.83.0:amd64 (1.83.0-3.2ubuntu2) ... 96s Selecting previously unselected package libboost-program-options1.83.0:amd64. 96s Preparing to unpack .../018-libboost-program-options1.83.0_1.83.0-3.2ubuntu2_amd64.deb ... 96s Unpacking libboost-program-options1.83.0:amd64 (1.83.0-3.2ubuntu2) ... 96s Selecting previously unselected package libboost-thread1.83.0:amd64. 96s Preparing to unpack .../019-libboost-thread1.83.0_1.83.0-3.2ubuntu2_amd64.deb ... 96s Unpacking libboost-thread1.83.0:amd64 (1.83.0-3.2ubuntu2) ... 96s Selecting previously unselected package libprotobuf32t64:amd64. 96s Preparing to unpack .../020-libprotobuf32t64_3.21.12-9ubuntu1_amd64.deb ... 96s Unpacking libprotobuf32t64:amd64 (3.21.12-9ubuntu1) ... 96s Selecting previously unselected package berkeley-express. 96s Preparing to unpack .../021-berkeley-express_1.5.3+dfsg-3build5_amd64.deb ... 96s Unpacking berkeley-express (1.5.3+dfsg-3build5) ... 96s Selecting previously unselected package ca-certificates-java. 96s Preparing to unpack .../022-ca-certificates-java_20240118_all.deb ... 96s Unpacking ca-certificates-java (20240118) ... 96s Selecting previously unselected package libdconf1:amd64. 96s Preparing to unpack .../023-libdconf1_0.40.0-4build2_amd64.deb ... 96s Unpacking libdconf1:amd64 (0.40.0-4build2) ... 96s Selecting previously unselected package dconf-service. 96s Preparing to unpack .../024-dconf-service_0.40.0-4build2_amd64.deb ... 96s Unpacking dconf-service (0.40.0-4build2) ... 96s Selecting previously unselected package dconf-gsettings-backend:amd64. 96s Preparing to unpack .../025-dconf-gsettings-backend_0.40.0-4build2_amd64.deb ... 96s Unpacking dconf-gsettings-backend:amd64 (0.40.0-4build2) ... 96s Selecting previously unselected package java-common. 96s Preparing to unpack .../026-java-common_0.76_all.deb ... 96s Unpacking java-common (0.76) ... 96s Selecting previously unselected package liblcms2-2:amd64. 96s Preparing to unpack .../027-liblcms2-2_2.14-2build1_amd64.deb ... 96s Unpacking liblcms2-2:amd64 (2.14-2build1) ... 96s Selecting previously unselected package libpcsclite1:amd64. 96s Preparing to unpack .../028-libpcsclite1_2.3.0-1_amd64.deb ... 96s Unpacking libpcsclite1:amd64 (2.3.0-1) ... 96s Selecting previously unselected package openjdk-21-jre-headless:amd64. 96s Preparing to unpack .../029-openjdk-21-jre-headless_21.0.5+11-1_amd64.deb ... 96s Unpacking openjdk-21-jre-headless:amd64 (21.0.5+11-1) ... 97s Selecting previously unselected package default-jre-headless. 97s Preparing to unpack .../030-default-jre-headless_2%3a1.21-76_amd64.deb ... 97s Unpacking default-jre-headless (2:1.21-76) ... 98s Selecting previously unselected package libatk1.0-0t64:amd64. 98s Preparing to unpack .../031-libatk1.0-0t64_2.54.0-1_amd64.deb ... 98s Unpacking libatk1.0-0t64:amd64 (2.54.0-1) ... 98s Selecting previously unselected package libxi6:amd64. 98s Preparing to unpack .../032-libxi6_2%3a1.8.2-1_amd64.deb ... 98s Unpacking libxi6:amd64 (2:1.8.2-1) ... 98s Selecting previously unselected package libatspi2.0-0t64:amd64. 98s Preparing to unpack .../033-libatspi2.0-0t64_2.54.0-1_amd64.deb ... 98s Unpacking libatspi2.0-0t64:amd64 (2.54.0-1) ... 98s Selecting previously unselected package libatk-bridge2.0-0t64:amd64. 98s Preparing to unpack .../034-libatk-bridge2.0-0t64_2.54.0-1_amd64.deb ... 98s Unpacking libatk-bridge2.0-0t64:amd64 (2.54.0-1) ... 98s Selecting previously unselected package fonts-dejavu-mono. 98s Preparing to unpack .../035-fonts-dejavu-mono_2.37-8_all.deb ... 98s Unpacking fonts-dejavu-mono (2.37-8) ... 98s Selecting previously unselected package fonts-dejavu-core. 98s Preparing to unpack .../036-fonts-dejavu-core_2.37-8_all.deb ... 98s Unpacking fonts-dejavu-core (2.37-8) ... 98s Selecting previously unselected package fontconfig-config. 98s Preparing to unpack .../037-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 98s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 98s Selecting previously unselected package libfontconfig1:amd64. 98s Preparing to unpack .../038-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 98s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 98s Selecting previously unselected package libpixman-1-0:amd64. 98s Preparing to unpack .../039-libpixman-1-0_0.42.2-1build1_amd64.deb ... 98s Unpacking libpixman-1-0:amd64 (0.42.2-1build1) ... 98s Selecting previously unselected package libxcb-render0:amd64. 98s Preparing to unpack .../040-libxcb-render0_1.17.0-2_amd64.deb ... 98s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 98s Selecting previously unselected package libxcb-shm0:amd64. 98s Preparing to unpack .../041-libxcb-shm0_1.17.0-2_amd64.deb ... 98s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 98s Selecting previously unselected package libxrender1:amd64. 98s Preparing to unpack .../042-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 98s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 98s Selecting previously unselected package libcairo2:amd64. 98s Preparing to unpack .../043-libcairo2_1.18.2-2_amd64.deb ... 98s Unpacking libcairo2:amd64 (1.18.2-2) ... 98s Selecting previously unselected package libcairo-gobject2:amd64. 98s Preparing to unpack .../044-libcairo-gobject2_1.18.2-2_amd64.deb ... 98s Unpacking libcairo-gobject2:amd64 (1.18.2-2) ... 98s Selecting previously unselected package libcolord2:amd64. 98s Preparing to unpack .../045-libcolord2_1.4.7-1build2_amd64.deb ... 98s Unpacking libcolord2:amd64 (1.4.7-1build2) ... 98s Selecting previously unselected package libavahi-common-data:amd64. 98s Preparing to unpack .../046-libavahi-common-data_0.8-13ubuntu6_amd64.deb ... 98s Unpacking libavahi-common-data:amd64 (0.8-13ubuntu6) ... 98s Selecting previously unselected package libavahi-common3:amd64. 98s Preparing to unpack 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previously unselected package libxrandr2:amd64. 99s Preparing to unpack .../068-libxrandr2_2%3a1.5.4-1_amd64.deb ... 99s Unpacking libxrandr2:amd64 (2:1.5.4-1) ... 99s Selecting previously unselected package libgtk-3-common. 99s Preparing to unpack .../069-libgtk-3-common_3.24.43-3ubuntu2_all.deb ... 99s Unpacking libgtk-3-common (3.24.43-3ubuntu2) ... 99s Selecting previously unselected package libgtk-3-0t64:amd64. 99s Preparing to unpack .../070-libgtk-3-0t64_3.24.43-3ubuntu2_amd64.deb ... 99s Unpacking libgtk-3-0t64:amd64 (3.24.43-3ubuntu2) ... 99s Selecting previously unselected package libglvnd0:amd64. 100s Preparing to unpack .../071-libglvnd0_1.7.0-1build1_amd64.deb ... 100s Unpacking libglvnd0:amd64 (1.7.0-1build1) ... 100s Selecting previously unselected package libglapi-mesa:amd64. 100s Preparing to unpack .../072-libglapi-mesa_24.2.3-1ubuntu1_amd64.deb ... 100s Unpacking libglapi-mesa:amd64 (24.2.3-1ubuntu1) ... 100s Selecting previously unselected package libx11-xcb1:amd64. 100s Preparing to unpack .../073-libx11-xcb1_2%3a1.8.7-1build1_amd64.deb ... 100s Unpacking libx11-xcb1:amd64 (2:1.8.7-1build1) ... 100s Selecting previously unselected package libxcb-dri2-0:amd64. 100s Preparing to unpack .../074-libxcb-dri2-0_1.17.0-2_amd64.deb ... 100s Unpacking libxcb-dri2-0:amd64 (1.17.0-2) ... 100s Selecting previously unselected package libxcb-dri3-0:amd64. 100s Preparing to unpack .../075-libxcb-dri3-0_1.17.0-2_amd64.deb ... 100s Unpacking libxcb-dri3-0:amd64 (1.17.0-2) ... 100s Selecting previously unselected package libxcb-glx0:amd64. 100s Preparing to unpack .../076-libxcb-glx0_1.17.0-2_amd64.deb ... 100s Unpacking libxcb-glx0:amd64 (1.17.0-2) ... 100s Selecting previously unselected package libxcb-present0:amd64. 100s Preparing to unpack .../077-libxcb-present0_1.17.0-2_amd64.deb ... 100s Unpacking libxcb-present0:amd64 (1.17.0-2) ... 100s Selecting previously unselected package libxcb-randr0:amd64. 100s Preparing to unpack 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Unpacking libdrm-amdgpu1:amd64 (2.4.122-1) ... 100s Selecting previously unselected package libpciaccess0:amd64. 100s Preparing to unpack .../084-libpciaccess0_0.17-3build1_amd64.deb ... 100s Unpacking libpciaccess0:amd64 (0.17-3build1) ... 100s Selecting previously unselected package libdrm-intel1:amd64. 100s Preparing to unpack .../085-libdrm-intel1_2.4.122-1_amd64.deb ... 100s Unpacking libdrm-intel1:amd64 (2.4.122-1) ... 100s Selecting previously unselected package libdrm-radeon1:amd64. 100s Preparing to unpack .../086-libdrm-radeon1_2.4.122-1_amd64.deb ... 100s Unpacking libdrm-radeon1:amd64 (2.4.122-1) ... 100s Selecting previously unselected package mesa-libgallium:amd64. 100s Preparing to unpack .../087-mesa-libgallium_24.2.3-1ubuntu1_amd64.deb ... 100s Unpacking mesa-libgallium:amd64 (24.2.3-1ubuntu1) ... 100s Selecting previously unselected package libvulkan1:amd64. 100s Preparing to unpack .../088-libvulkan1_1.3.290.0-1_amd64.deb ... 100s Unpacking libvulkan1:amd64 (1.3.290.0-1) ... 100s Selecting previously unselected package libwayland-server0:amd64. 100s Preparing to unpack .../089-libwayland-server0_1.23.0-1_amd64.deb ... 100s Unpacking libwayland-server0:amd64 (1.23.0-1) ... 101s Selecting previously unselected package libgbm1:amd64. 101s Preparing to unpack .../090-libgbm1_24.2.3-1ubuntu1_amd64.deb ... 101s Unpacking libgbm1:amd64 (24.2.3-1ubuntu1) ... 101s Selecting previously unselected package libgl1-mesa-dri:amd64. 101s Preparing to unpack .../091-libgl1-mesa-dri_24.2.3-1ubuntu1_amd64.deb ... 101s Unpacking libgl1-mesa-dri:amd64 (24.2.3-1ubuntu1) ... 101s Selecting previously unselected package libglx-mesa0:amd64. 101s Preparing to unpack .../092-libglx-mesa0_24.2.3-1ubuntu1_amd64.deb ... 101s Unpacking libglx-mesa0:amd64 (24.2.3-1ubuntu1) ... 101s Selecting previously unselected package libglx0:amd64. 101s Preparing to unpack .../093-libglx0_1.7.0-1build1_amd64.deb ... 101s Unpacking libglx0:amd64 (1.7.0-1build1) ... 101s Selecting previously unselected package libgl1:amd64. 101s Preparing to unpack .../094-libgl1_1.7.0-1build1_amd64.deb ... 101s Unpacking libgl1:amd64 (1.7.0-1build1) ... 101s Selecting previously unselected package libasound2-data. 101s Preparing to unpack .../095-libasound2-data_1.2.12-1_all.deb ... 101s Unpacking libasound2-data (1.2.12-1) ... 101s Selecting previously unselected package libasound2t64:amd64. 101s Preparing to unpack .../096-libasound2t64_1.2.12-1_amd64.deb ... 101s Unpacking libasound2t64:amd64 (1.2.12-1) ... 101s Selecting previously unselected package libgif7:amd64. 101s Preparing to unpack .../097-libgif7_5.2.2-1ubuntu1_amd64.deb ... 101s Unpacking libgif7:amd64 (5.2.2-1ubuntu1) ... 101s Selecting previously unselected package x11-common. 101s Preparing to unpack .../098-x11-common_1%3a7.7+23ubuntu3_all.deb ... 101s Unpacking x11-common (1:7.7+23ubuntu3) ... 101s Selecting previously unselected package libxtst6:amd64. 101s Preparing to unpack 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previously unselected package libhts3t64:amd64. 102s Preparing to unpack .../110-libhts3t64_1.20+ds-1_amd64.deb ... 102s Unpacking libhts3t64:amd64 (1.20+ds-1) ... 102s Selecting previously unselected package libjellyfish-2.0-2:amd64. 102s Preparing to unpack .../111-libjellyfish-2.0-2_2.3.1-3build2_amd64.deb ... 102s Unpacking libjellyfish-2.0-2:amd64 (2.3.1-3build2) ... 102s Selecting previously unselected package jellyfish. 102s Preparing to unpack .../112-jellyfish_2.3.1-3build2_amd64.deb ... 102s Unpacking jellyfish (2.3.1-3build2) ... 102s Selecting previously unselected package kallisto. 102s Preparing to unpack .../113-kallisto_0.48.0+dfsg-4build1_amd64.deb ... 102s Unpacking kallisto (0.48.0+dfsg-4build1) ... 102s Selecting previously unselected package libapache-pom-java. 102s Preparing to unpack .../114-libapache-pom-java_33-2_all.deb ... 102s Unpacking libapache-pom-java (33-2) ... 102s Selecting previously unselected package libasan8:amd64. 102s Preparing to unpack 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Selecting previously unselected package libio-string-perl. 103s Preparing to unpack .../131-libio-string-perl_1.08-4_all.deb ... 103s Unpacking libio-string-perl (1.08-4) ... 103s Selecting previously unselected package liblatex-tounicode-perl. 103s Preparing to unpack .../132-liblatex-tounicode-perl_0.54-2_all.deb ... 103s Unpacking liblatex-tounicode-perl (0.54-2) ... 103s Selecting previously unselected package libbibtex-parser-perl. 103s Preparing to unpack .../133-libbibtex-parser-perl_1.04+dfsg-1_all.deb ... 103s Unpacking libbibtex-parser-perl (1.04+dfsg-1) ... 103s Selecting previously unselected package libblas3:amd64. 103s Preparing to unpack .../134-libblas3_3.12.0-3build2_amd64.deb ... 103s Unpacking libblas3:amd64 (3.12.0-3build2) ... 103s Selecting previously unselected package libgomp1:amd64. 103s Preparing to unpack .../135-libgomp1_14.2.0-7ubuntu1_amd64.deb ... 103s Unpacking libgomp1:amd64 (14.2.0-7ubuntu1) ... 103s Selecting previously unselected package libitm1:amd64. 103s Preparing to unpack .../136-libitm1_14.2.0-7ubuntu1_amd64.deb ... 103s Unpacking libitm1:amd64 (14.2.0-7ubuntu1) ... 103s Selecting previously unselected package liblsan0:amd64. 103s Preparing to unpack .../137-liblsan0_14.2.0-7ubuntu1_amd64.deb ... 103s Unpacking liblsan0:amd64 (14.2.0-7ubuntu1) ... 103s Selecting previously unselected package libtsan2:amd64. 103s Preparing to unpack .../138-libtsan2_14.2.0-7ubuntu1_amd64.deb ... 103s Unpacking libtsan2:amd64 (14.2.0-7ubuntu1) ... 103s Selecting previously unselected package libubsan1:amd64. 103s Preparing to unpack .../139-libubsan1_14.2.0-7ubuntu1_amd64.deb ... 103s Unpacking libubsan1:amd64 (14.2.0-7ubuntu1) ... 104s Selecting previously unselected package libhwasan0:amd64. 104s Preparing to unpack .../140-libhwasan0_14.2.0-7ubuntu1_amd64.deb ... 104s Unpacking libhwasan0:amd64 (14.2.0-7ubuntu1) ... 104s Selecting previously unselected package libquadmath0:amd64. 104s Preparing to unpack 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libboost-iostreams1.83.0:amd64. 108s Preparing to unpack .../146-libboost-iostreams1.83.0_1.83.0-3.2ubuntu2_amd64.deb ... 108s Unpacking libboost-iostreams1.83.0:amd64 (1.83.0-3.2ubuntu2) ... 108s Selecting previously unselected package libclone-perl:amd64. 108s Preparing to unpack .../147-libclone-perl_0.47-1_amd64.deb ... 108s Unpacking libclone-perl:amd64 (0.47-1) ... 108s Selecting previously unselected package libcommons-compress-java. 108s Preparing to unpack .../148-libcommons-compress-java_1.25.0-1_all.deb ... 108s Unpacking libcommons-compress-java (1.25.0-1) ... 108s Selecting previously unselected package libcommons-io-java. 108s Preparing to unpack .../149-libcommons-io-java_2.16.1-1_all.deb ... 108s Unpacking libcommons-io-java (2.16.1-1) ... 108s Selecting previously unselected package libcommons-jexl2-java. 108s Preparing to unpack .../150-libcommons-jexl2-java_2.1.1-6_all.deb ... 108s Unpacking libcommons-jexl2-java (2.1.1-6) ... 108s Selecting previously unselected package libcommons-math3-java. 108s Preparing to unpack .../151-libcommons-math3-java_3.6.1-3_all.deb ... 108s Unpacking libcommons-math3-java (3.6.1-3) ... 108s Selecting previously unselected package libencode-locale-perl. 108s Preparing to unpack .../152-libencode-locale-perl_1.05-3_all.deb ... 108s Unpacking libencode-locale-perl (1.05-3) ... 108s Selecting previously unselected package libjsr305-java. 108s Preparing to unpack .../153-libjsr305-java_0.1~+svn49-11_all.deb ... 108s Unpacking libjsr305-java (0.1~+svn49-11) ... 108s Selecting previously unselected package libguava-java. 108s Preparing to unpack .../154-libguava-java_32.0.1-1_all.deb ... 108s Unpacking libguava-java (32.0.1-1) ... 108s Selecting previously unselected package liberror-prone-java. 108s Preparing to unpack .../155-liberror-prone-java_2.18.0-1_all.deb ... 108s Unpacking liberror-prone-java (2.18.0-1) ... 108s Selecting previously unselected package libtimedate-perl. 108s Preparing to unpack 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109s Unpacking ncbi-vdb-data (3.0.2+dfsg-2build2) ... 109s Selecting previously unselected package libncbi-vdb3:amd64. 109s Preparing to unpack .../167-libncbi-vdb3_3.0.2+dfsg-2build2_amd64.deb ... 109s Unpacking libncbi-vdb3:amd64 (3.0.2+dfsg-2build2) ... 109s Selecting previously unselected package libncbi-ngs3:amd64. 109s Preparing to unpack .../168-libncbi-ngs3_3.0.3+dfsg-9ubuntu1_amd64.deb ... 109s Unpacking libncbi-ngs3:amd64 (3.0.3+dfsg-9ubuntu1) ... 109s Selecting previously unselected package libngs-jni:amd64. 109s Preparing to unpack .../169-libngs-jni_3.0.3+dfsg-9ubuntu1_amd64.deb ... 109s Unpacking libngs-jni:amd64 (3.0.3+dfsg-9ubuntu1) ... 109s Selecting previously unselected package libngs-java:amd64. 109s Preparing to unpack .../170-libngs-java_3.0.3+dfsg-9ubuntu1_amd64.deb ... 109s Unpacking libngs-java:amd64 (3.0.3+dfsg-9ubuntu1) ... 109s Selecting previously unselected package librhino-java. 109s Preparing to unpack .../171-librhino-java_1.7.14-2.1_all.deb ... 109s Unpacking librhino-java (1.7.14-2.1) ... 109s Selecting previously unselected package libsnappy1v5:amd64. 109s Preparing to unpack .../172-libsnappy1v5_1.2.1-1_amd64.deb ... 109s Unpacking libsnappy1v5:amd64 (1.2.1-1) ... 109s Selecting previously unselected package libsnappy-jni. 109s Preparing to unpack .../173-libsnappy-jni_1.1.10.5-2_amd64.deb ... 109s Unpacking libsnappy-jni (1.1.10.5-2) ... 109s Selecting previously unselected package libsnappy-java. 109s Preparing to unpack .../174-libsnappy-java_1.1.10.5-2_all.deb ... 109s Unpacking libsnappy-java (1.1.10.5-2) ... 109s Selecting previously unselected package libhtsjdk-java. 109s Preparing to unpack .../175-libhtsjdk-java_4.1.0+dfsg-2_all.deb ... 109s Unpacking libhtsjdk-java (4.1.0+dfsg-2) ... 109s Selecting previously unselected package libgkl-java. 109s Preparing to unpack .../176-libgkl-java_0.8.11+dfsg-2build1_all.deb ... 109s Unpacking libgkl-java (0.8.11+dfsg-2build1) ... 109s Selecting previously unselected package libhtml-tagset-perl. 109s Preparing to unpack .../177-libhtml-tagset-perl_3.24-1_all.deb ... 109s Unpacking libhtml-tagset-perl (3.24-1) ... 109s Selecting previously unselected package liburi-perl. 109s Preparing to unpack .../178-liburi-perl_5.30-1_all.deb ... 109s Unpacking liburi-perl (5.30-1) ... 110s Selecting previously unselected package libhtml-parser-perl:amd64. 110s Preparing to unpack .../179-libhtml-parser-perl_3.83-1build1_amd64.deb ... 110s Unpacking libhtml-parser-perl:amd64 (3.83-1build1) ... 110s Selecting previously unselected package libhtml-tree-perl. 110s Preparing to unpack .../180-libhtml-tree-perl_5.07-3_all.deb ... 110s Unpacking libhtml-tree-perl (5.07-3) ... 110s Selecting previously unselected package libio-html-perl. 110s Preparing to unpack .../181-libio-html-perl_1.004-3_all.deb ... 110s Unpacking libio-html-perl (1.004-3) ... 110s Selecting previously unselected package liblwp-mediatypes-perl. 110s Preparing to unpack .../182-liblwp-mediatypes-perl_6.04-2_all.deb ... 110s Unpacking liblwp-mediatypes-perl (6.04-2) ... 110s Selecting previously unselected package libhttp-message-perl. 110s Preparing to unpack .../183-libhttp-message-perl_6.46-1ubuntu1_all.deb ... 110s Unpacking libhttp-message-perl (6.46-1ubuntu1) ... 110s Selecting previously unselected package libhttp-cookies-perl. 110s Preparing to unpack .../184-libhttp-cookies-perl_6.11-1_all.deb ... 110s Unpacking libhttp-cookies-perl (6.11-1) ... 110s Selecting previously unselected package libhttp-negotiate-perl. 110s Preparing to unpack .../185-libhttp-negotiate-perl_6.01-2_all.deb ... 110s Unpacking libhttp-negotiate-perl (6.01-2) ... 110s Selecting previously unselected package libhwloc15:amd64. 110s Preparing to unpack .../186-libhwloc15_2.11.0-2_amd64.deb ... 110s Unpacking libhwloc15:amd64 (2.11.0-2) ... 110s Selecting previously unselected package libice6:amd64. 110s Preparing to unpack .../187-libice6_2%3a1.0.10-1build3_amd64.deb ... 110s Unpacking libice6:amd64 (2:1.0.10-1build3) ... 110s Selecting previously unselected package perl-openssl-defaults:amd64. 110s Preparing to unpack .../188-perl-openssl-defaults_7build3_amd64.deb ... 110s Unpacking perl-openssl-defaults:amd64 (7build3) ... 110s Selecting previously unselected package libnet-ssleay-perl:amd64. 110s Preparing to unpack .../189-libnet-ssleay-perl_1.94-2_amd64.deb ... 110s Unpacking libnet-ssleay-perl:amd64 (1.94-2) ... 110s Selecting previously unselected package libio-socket-ssl-perl. 110s Preparing to unpack .../190-libio-socket-ssl-perl_2.088-1_all.deb ... 110s Unpacking libio-socket-ssl-perl (2.088-1) ... 110s Selecting previously unselected package libjemalloc2:amd64. 110s Preparing to unpack .../191-libjemalloc2_5.3.0-2build1_amd64.deb ... 110s Unpacking libjemalloc2:amd64 (5.3.0-2build1) ... 110s Selecting previously unselected package libjs-bootstrap. 110s Preparing to unpack .../192-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 110s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 110s Selecting previously unselected package libjs-popper.js. 110s Preparing to unpack .../193-libjs-popper.js_1.16.1+ds-6_all.deb ... 110s Unpacking libjs-popper.js (1.16.1+ds-6) ... 110s Selecting previously unselected package libjs-bootstrap4. 110s Preparing to unpack .../194-libjs-bootstrap4_4.6.1+dfsg1-4_all.deb ... 110s Unpacking libjs-bootstrap4 (4.6.1+dfsg1-4) ... 110s Selecting previously unselected package libjs-d3. 110s Preparing to unpack .../195-libjs-d3_3.5.17-4_all.deb ... 110s Unpacking libjs-d3 (3.5.17-4) ... 111s Selecting previously unselected package libjs-es5-shim. 111s Preparing to unpack .../196-libjs-es5-shim_4.6.7-2_all.deb ... 111s Unpacking libjs-es5-shim (4.6.7-2) ... 111s Selecting previously unselected package libjs-highlight.js. 111s Preparing to unpack .../197-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 111s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 111s Selecting previously unselected package libjs-jquery. 111s Preparing to unpack .../198-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 111s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 111s Selecting previously unselected package libjs-jquery-datatables. 111s Preparing to unpack .../199-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 111s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 111s Selecting previously unselected package libjs-sifter.js. 111s Preparing to unpack .../200-libjs-sifter.js_0.6.0+dfsg-3_all.deb ... 111s Unpacking libjs-sifter.js (0.6.0+dfsg-3) ... 111s Selecting previously unselected package libjs-microplugin.js. 111s Preparing to unpack .../201-libjs-microplugin.js_0.0.3+dfsg-1.1_all.deb ... 111s Unpacking libjs-microplugin.js (0.0.3+dfsg-1.1) ... 111s Selecting previously unselected package libjs-jquery-selectize.js. 111s Preparing to unpack .../202-libjs-jquery-selectize.js_0.12.6+dfsg-1.1_all.deb ... 111s Unpacking libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... 111s Selecting previously unselected package libjs-jquery-ui. 111s Preparing to unpack .../203-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 111s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 111s Selecting previously unselected package libjs-json. 111s Preparing to unpack .../204-libjs-json_0~20221030+~1.0.8-1_all.deb ... 111s Unpacking libjs-json (0~20221030+~1.0.8-1) ... 111s Selecting previously unselected package libjs-lunr. 111s Preparing to unpack .../205-libjs-lunr_2.3.9~dfsg-2_all.deb ... 111s Unpacking libjs-lunr (2.3.9~dfsg-2) ... 111s Selecting previously unselected package libjs-prettify. 111s Preparing to unpack .../206-libjs-prettify_2015.12.04+dfsg-1.1_all.deb ... 111s Unpacking libjs-prettify (2015.12.04+dfsg-1.1) ... 111s Selecting previously unselected package libjs-underscore. 111s Preparing to unpack .../207-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 111s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 111s Selecting previously unselected package libjs-sphinxdoc. 111s Preparing to unpack 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112s Unpacking libnet-http-perl (6.23-1) ... 112s Selecting previously unselected package libtry-tiny-perl. 112s Preparing to unpack .../214-libtry-tiny-perl_0.31-2_all.deb ... 112s Unpacking libtry-tiny-perl (0.31-2) ... 112s Selecting previously unselected package libwww-robotrules-perl. 112s Preparing to unpack .../215-libwww-robotrules-perl_6.02-1_all.deb ... 112s Unpacking libwww-robotrules-perl (6.02-1) ... 112s Selecting previously unselected package libwww-perl. 112s Preparing to unpack .../216-libwww-perl_6.77-1_all.deb ... 112s Unpacking libwww-perl (6.77-1) ... 112s Selecting previously unselected package liblwp-protocol-https-perl. 112s Preparing to unpack .../217-liblwp-protocol-https-perl_6.14-1_all.deb ... 112s Unpacking liblwp-protocol-https-perl (6.14-1) ... 112s Selecting previously unselected package libmpfi0:amd64. 112s Preparing to unpack .../218-libmpfi0_1.5.4+ds-3_amd64.deb ... 112s Unpacking libmpfi0:amd64 (1.5.4+ds-3) ... 112s Selecting previously unselected package libpaper1:amd64. 112s Preparing to unpack .../219-libpaper1_1.1.29build1_amd64.deb ... 112s Unpacking libpaper1:amd64 (1.1.29build1) ... 112s Selecting previously unselected package libpaper-utils. 112s Preparing to unpack .../220-libpaper-utils_1.1.29build1_amd64.deb ... 112s Unpacking libpaper-utils (1.1.29build1) ... 112s Selecting previously unselected package libpicard-java. 112s Preparing to unpack .../221-libpicard-java_3.1.1+dfsg-1_all.deb ... 112s Unpacking libpicard-java (3.1.1+dfsg-1) ... 112s Selecting previously unselected package libpotrace0:amd64. 112s Preparing to unpack .../222-libpotrace0_1.16-2build1_amd64.deb ... 112s Unpacking libpotrace0:amd64 (1.16-2build1) ... 112s Selecting previously unselected package libptexenc1:amd64. 112s Preparing to unpack .../223-libptexenc1_2024.20240313.70630+ds-4_amd64.deb ... 112s Unpacking libptexenc1:amd64 (2024.20240313.70630+ds-4) ... 112s Selecting previously unselected package libsm6:amd64. 112s Preparing to unpack .../224-libsm6_2%3a1.2.3-1build3_amd64.deb ... 112s Unpacking libsm6:amd64 (2:1.2.3-1build3) ... 112s Selecting previously unselected package libstaden-read14t64:amd64. 112s Preparing to unpack .../225-libstaden-read14t64_1.15.0-1.1build2_amd64.deb ... 112s Unpacking libstaden-read14t64:amd64 (1.15.0-1.1build2) ... 112s Selecting previously unselected package libsynctex2:amd64. 112s Preparing to unpack .../226-libsynctex2_2024.20240313.70630+ds-4_amd64.deb ... 112s Unpacking libsynctex2:amd64 (2024.20240313.70630+ds-4) ... 112s Selecting previously unselected package libtbbmalloc2:amd64. 112s Preparing to unpack .../227-libtbbmalloc2_2021.12.0-1ubuntu2_amd64.deb ... 112s Unpacking libtbbmalloc2:amd64 (2021.12.0-1ubuntu2) ... 112s Selecting previously unselected package libtbbbind-2-5:amd64. 112s Preparing to unpack .../228-libtbbbind-2-5_2021.12.0-1ubuntu2_amd64.deb ... 112s Unpacking libtbbbind-2-5:amd64 (2021.12.0-1ubuntu2) ... 112s Selecting previously unselected package libtbb12:amd64. 112s Preparing to unpack .../229-libtbb12_2021.12.0-1ubuntu2_amd64.deb ... 112s Unpacking libtbb12:amd64 (2021.12.0-1ubuntu2) ... 112s Selecting previously unselected package libtcl8.6:amd64. 112s Preparing to unpack .../230-libtcl8.6_8.6.14+dfsg-1build1_amd64.deb ... 112s Unpacking libtcl8.6:amd64 (8.6.14+dfsg-1build1) ... 112s Selecting previously unselected package libteckit0:amd64. 112s Preparing to unpack .../231-libteckit0_2.5.12+ds1-1_amd64.deb ... 112s Unpacking libteckit0:amd64 (2.5.12+ds1-1) ... 112s Selecting previously unselected package libtexlua53-5:amd64. 112s Preparing to unpack .../232-libtexlua53-5_2024.20240313.70630+ds-4_amd64.deb ... 112s Unpacking libtexlua53-5:amd64 (2024.20240313.70630+ds-4) ... 112s Selecting previously unselected package libxft2:amd64. 112s Preparing to unpack .../233-libxft2_2.3.6-1build1_amd64.deb ... 112s Unpacking libxft2:amd64 (2.3.6-1build1) ... 112s Selecting previously unselected package libxss1:amd64. 112s Preparing to unpack .../234-libxss1_1%3a1.2.3-1build3_amd64.deb ... 112s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 112s Selecting previously unselected package libtk8.6:amd64. 112s Preparing to unpack .../235-libtk8.6_8.6.14-1build1_amd64.deb ... 112s Unpacking libtk8.6:amd64 (8.6.14-1build1) ... 113s Selecting previously unselected package libxt6t64:amd64. 113s Preparing to unpack .../236-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ... 113s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ... 113s Selecting previously unselected package libxmu6:amd64. 113s Preparing to unpack .../237-libxmu6_2%3a1.1.3-3build2_amd64.deb ... 113s Unpacking libxmu6:amd64 (2:1.1.3-3build2) ... 113s Selecting previously unselected package libxpm4:amd64. 113s Preparing to unpack .../238-libxpm4_1%3a3.5.17-1build2_amd64.deb ... 113s Unpacking libxpm4:amd64 (1:3.5.17-1build2) ... 113s Selecting previously unselected package libxaw7:amd64. 113s Preparing to unpack .../239-libxaw7_2%3a1.0.14-1build2_amd64.deb ... 113s Unpacking libxaw7:amd64 (2:1.0.14-1build2) ... 113s Selecting previously unselected package libzzip-0-13t64:amd64. 113s Preparing to unpack .../240-libzzip-0-13t64_0.13.72+dfsg.1-1.2build1_amd64.deb ... 113s Unpacking libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.2build1) ... 113s Selecting previously unselected package zip. 113s Preparing to unpack .../241-zip_3.0-14_amd64.deb ... 113s Unpacking zip (3.0-14) ... 113s Selecting previously unselected package unzip. 113s Preparing to unpack .../242-unzip_6.0-28ubuntu6_amd64.deb ... 113s Unpacking unzip (6.0-28ubuntu6) ... 113s Selecting previously unselected package xdg-utils. 113s Preparing to unpack .../243-xdg-utils_1.2.1-0ubuntu1_all.deb ... 113s Unpacking xdg-utils (1.2.1-0ubuntu1) ... 113s Selecting previously unselected package r-base-core. 113s Preparing to unpack .../244-r-base-core_4.4.1-1_amd64.deb ... 113s Unpacking r-base-core (4.4.1-1) ... 114s Selecting previously unselected package r-cran-littler. 114s Preparing to unpack .../245-r-cran-littler_0.3.20-1_amd64.deb ... 114s Unpacking r-cran-littler (0.3.20-1) ... 114s Selecting previously unselected package littler. 114s Preparing to unpack .../246-littler_0.3.20-1_all.deb ... 114s Unpacking littler (0.3.20-1) ... 114s Selecting previously unselected package ncbi-data. 114s Preparing to unpack .../247-ncbi-data_6.1.20170106+dfsg2-3_all.deb ... 114s Unpacking ncbi-data (6.1.20170106+dfsg2-3) ... 114s Selecting previously unselected package ncbi-blast+. 114s Preparing to unpack .../248-ncbi-blast+_2.16.0+ds-6_amd64.deb ... 114s Unpacking ncbi-blast+ (2.16.0+ds-6) ... 114s Selecting previously unselected package node-bootstrap-sass. 114s Preparing to unpack .../249-node-bootstrap-sass_3.4.3-2_all.deb ... 114s Unpacking node-bootstrap-sass (3.4.3-2) ... 114s Selecting previously unselected package node-html5shiv. 114s Preparing to unpack .../250-node-html5shiv_3.7.3+dfsg-5_all.deb ... 114s Unpacking node-html5shiv (3.7.3+dfsg-5) ... 114s Selecting previously unselected package node-normalize.css. 114s Preparing to unpack .../251-node-normalize.css_8.0.1-5_all.deb ... 114s Unpacking node-normalize.css (8.0.1-5) ... 114s Selecting previously unselected package pandoc-data. 114s Preparing to unpack .../252-pandoc-data_3.1.11.1-3_all.deb ... 114s Unpacking pandoc-data (3.1.11.1-3) ... 114s Selecting previously unselected package pandoc. 114s Preparing to unpack .../253-pandoc_3.1.11.1+ds-2_amd64.deb ... 114s Unpacking pandoc (3.1.11.1+ds-2) ... 116s Selecting previously unselected package parafly. 116s Preparing to unpack .../254-parafly_0.1.0-4_amd64.deb ... 116s Unpacking parafly (0.1.0-4) ... 116s Selecting previously unselected package python3-hisat2. 116s Preparing to unpack .../255-python3-hisat2_2.2.1-5_all.deb ... 116s Unpacking python3-hisat2 (2.2.1-5) ... 116s Selecting previously unselected package python3-numpy. 116s Preparing to unpack .../256-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 116s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 116s Selecting previously unselected package python3-pysam. 116s Preparing to unpack .../257-python3-pysam_0.22.1+ds-2_amd64.deb ... 116s Unpacking python3-pysam (0.22.1+ds-2) ... 116s Selecting previously unselected package python3-htseq. 116s Preparing to unpack .../258-python3-htseq_2.0.5-2_amd64.deb ... 116s Unpacking python3-htseq (2.0.5-2) ... 116s Selecting previously unselected package r-bioc-biocgenerics. 116s Preparing to unpack .../259-r-bioc-biocgenerics_0.50.0-2_all.deb ... 116s Unpacking r-bioc-biocgenerics (0.50.0-2) ... 116s Selecting previously unselected package r-bioc-biobase. 116s Preparing to unpack .../260-r-bioc-biobase_2.64.0-4_amd64.deb ... 116s Unpacking r-bioc-biobase (2.64.0-4) ... 117s Selecting previously unselected package r-bioc-s4vectors. 117s Preparing to unpack .../261-r-bioc-s4vectors_0.42.1+dfsg-2_amd64.deb ... 117s Unpacking r-bioc-s4vectors (0.42.1+dfsg-2) ... 117s Selecting previously unselected package r-bioc-iranges. 117s Preparing to unpack .../262-r-bioc-iranges_2.38.1-1_amd64.deb ... 117s Unpacking r-bioc-iranges (2.38.1-1) ... 117s Selecting previously unselected package r-cran-dbi. 117s Preparing to unpack .../263-r-cran-dbi_1.2.3-1_all.deb ... 117s Unpacking r-cran-dbi (1.2.3-1) ... 117s Selecting previously unselected package r-cran-bit. 117s Preparing to unpack .../264-r-cran-bit_4.0.5-1_amd64.deb ... 117s Unpacking r-cran-bit (4.0.5-1) ... 117s Selecting previously unselected package r-cran-bit64. 117s Preparing to unpack .../265-r-cran-bit64_4.0.5-1_amd64.deb ... 117s Unpacking r-cran-bit64 (4.0.5-1) ... 117s Selecting previously unselected package r-cran-rlang. 117s Preparing to unpack .../266-r-cran-rlang_1.1.4-1_amd64.deb ... 117s Unpacking r-cran-rlang (1.1.4-1) ... 117s Selecting previously unselected package r-cran-cli. 117s Preparing to unpack .../267-r-cran-cli_3.6.2-1_amd64.deb ... 117s Unpacking r-cran-cli (3.6.2-1) ... 117s Selecting previously unselected package r-cran-glue. 117s Preparing to unpack .../268-r-cran-glue_1.7.0-1_amd64.deb ... 117s Unpacking r-cran-glue (1.7.0-1) ... 117s Selecting previously unselected package r-cran-lifecycle. 117s Preparing to unpack .../269-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 117s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 117s Selecting previously unselected package r-cran-vctrs. 117s Preparing to unpack .../270-r-cran-vctrs_0.6.5-1_amd64.deb ... 117s Unpacking r-cran-vctrs (0.6.5-1) ... 117s Selecting previously unselected package r-cran-blob. 117s Preparing to unpack .../271-r-cran-blob_1.2.4-1_all.deb ... 117s Unpacking r-cran-blob (1.2.4-1) ... 117s Selecting previously unselected package r-cran-fastmap. 117s Preparing to unpack .../272-r-cran-fastmap_1.1.1-1_amd64.deb ... 117s Unpacking r-cran-fastmap (1.1.1-1) ... 117s Selecting previously unselected package r-cran-cachem. 117s Preparing to unpack .../273-r-cran-cachem_1.0.8-1_amd64.deb ... 117s Unpacking r-cran-cachem (1.0.8-1) ... 117s Selecting previously unselected package r-cran-memoise. 117s Preparing to unpack .../274-r-cran-memoise_2.0.1-1_all.deb ... 117s Unpacking r-cran-memoise (2.0.1-1) ... 117s Selecting previously unselected package r-cran-pkgconfig. 117s Preparing to unpack .../275-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 117s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 117s Selecting previously unselected package r-cran-plogr. 117s Preparing to unpack .../276-r-cran-plogr_0.2.0-3build1_all.deb ... 117s Unpacking r-cran-plogr (0.2.0-3build1) ... 118s Selecting previously unselected package r-cran-cpp11. 118s Preparing to unpack .../277-r-cran-cpp11_0.4.7-1_all.deb ... 118s Unpacking r-cran-cpp11 (0.4.7-1) ... 118s Selecting previously unselected package r-cran-rsqlite. 118s Preparing to unpack .../278-r-cran-rsqlite_2.3.7-2_amd64.deb ... 118s Unpacking r-cran-rsqlite (2.3.7-2) ... 118s Selecting previously unselected package r-cran-curl. 118s Preparing to unpack .../279-r-cran-curl_5.2.1+dfsg-1_amd64.deb ... 118s Unpacking r-cran-curl (5.2.1+dfsg-1) ... 118s Selecting previously unselected package r-cran-jsonlite. 118s Preparing to unpack .../280-r-cran-jsonlite_1.8.8+dfsg-1_amd64.deb ... 118s Unpacking r-cran-jsonlite (1.8.8+dfsg-1) ... 118s Selecting previously unselected package r-cran-mime. 118s Preparing to unpack .../281-r-cran-mime_0.12-2_amd64.deb ... 118s Unpacking r-cran-mime (0.12-2) ... 118s Selecting previously unselected package r-cran-sys. 118s Preparing to unpack .../282-r-cran-sys_3.4.2-1_amd64.deb ... 118s Unpacking r-cran-sys (3.4.2-1) ... 118s Selecting previously unselected package r-cran-askpass. 118s Preparing to unpack .../283-r-cran-askpass_1.2.0-1_amd64.deb ... 118s Unpacking r-cran-askpass (1.2.0-1) ... 118s Selecting previously unselected package r-cran-openssl. 118s Preparing to unpack .../284-r-cran-openssl_2.2.0+dfsg-1_amd64.deb ... 118s Unpacking r-cran-openssl (2.2.0+dfsg-1) ... 118s Selecting previously unselected package r-cran-r6. 118s Preparing to unpack .../285-r-cran-r6_2.5.1-1_all.deb ... 118s Unpacking r-cran-r6 (2.5.1-1) ... 118s Selecting previously unselected package r-cran-httr. 118s Preparing to unpack .../286-r-cran-httr_1.4.7+dfsg-1_all.deb ... 118s Unpacking r-cran-httr (1.4.7+dfsg-1) ... 118s Selecting previously unselected package r-cran-png. 118s Preparing to unpack .../287-r-cran-png_0.1-8-1build2_amd64.deb ... 118s Unpacking r-cran-png (0.1-8-1build2) ... 118s Selecting previously unselected package zlib1g-dev:amd64. 118s Preparing to unpack .../288-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ... 118s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 118s Selecting previously unselected package r-bioc-zlibbioc. 118s Preparing to unpack .../289-r-bioc-zlibbioc_1.50.0+dfsg-2_all.deb ... 118s Unpacking r-bioc-zlibbioc (1.50.0+dfsg-2) ... 118s Selecting previously unselected package r-bioc-xvector. 118s Preparing to unpack .../290-r-bioc-xvector_0.44.0-1_amd64.deb ... 118s Unpacking r-bioc-xvector (0.44.0-1) ... 118s Selecting previously unselected package r-bioc-ucsc.utils. 118s Preparing to unpack .../291-r-bioc-ucsc.utils_1.0.0+ds-2_all.deb ... 118s Unpacking r-bioc-ucsc.utils (1.0.0+ds-2) ... 118s Selecting previously unselected package r-bioc-genomeinfodbdata. 118s Preparing to unpack .../292-r-bioc-genomeinfodbdata_1.2.12-1_all.deb ... 118s Unpacking r-bioc-genomeinfodbdata (1.2.12-1) ... 118s Selecting previously unselected package r-bioc-genomeinfodb. 118s Preparing to unpack .../293-r-bioc-genomeinfodb_1.40.1+dfsg-1_all.deb ... 118s Unpacking r-bioc-genomeinfodb (1.40.1+dfsg-1) ... 119s Selecting previously unselected package r-cran-crayon. 119s Preparing to unpack .../294-r-cran-crayon_1.5.2-1_all.deb ... 119s Unpacking r-cran-crayon (1.5.2-1) ... 119s Selecting previously unselected package r-bioc-biostrings. 119s Preparing to unpack .../295-r-bioc-biostrings_2.72.1+dfsg-1_amd64.deb ... 119s Unpacking r-bioc-biostrings (2.72.1+dfsg-1) ... 119s Selecting previously unselected package r-bioc-keggrest. 119s Preparing to unpack .../296-r-bioc-keggrest_1.44.1+dfsg-1_all.deb ... 119s Unpacking r-bioc-keggrest (1.44.1+dfsg-1) ... 119s Selecting previously unselected package r-bioc-annotationdbi. 119s Preparing to unpack .../297-r-bioc-annotationdbi_1.66.0-1_all.deb ... 119s Unpacking r-bioc-annotationdbi (1.66.0-1) ... 119s Selecting previously unselected package r-cran-xml. 119s Preparing to unpack .../298-r-cran-xml_3.99-0.17-1_amd64.deb ... 119s Unpacking r-cran-xml (3.99-0.17-1) ... 119s Selecting previously unselected package r-cran-xtable. 119s Preparing to unpack .../299-r-cran-xtable_1%3a1.8-4-2_all.deb ... 119s Unpacking r-cran-xtable (1:1.8-4-2) ... 119s Selecting previously unselected package r-bioc-annotate. 119s Preparing to unpack .../300-r-bioc-annotate_1.82.0+dfsg-1_all.deb ... 119s Unpacking r-bioc-annotate (1.82.0+dfsg-1) ... 119s Selecting previously unselected package r-cran-generics. 119s Preparing to unpack .../301-r-cran-generics_0.1.3-1_all.deb ... 119s Unpacking r-cran-generics (0.1.3-1) ... 119s Selecting previously unselected package r-cran-magrittr. 119s Preparing to unpack .../302-r-cran-magrittr_2.0.3-1_amd64.deb ... 119s Unpacking r-cran-magrittr (2.0.3-1) ... 119s Selecting previously unselected package r-cran-fansi. 119s Preparing to unpack .../303-r-cran-fansi_1.0.5-1_amd64.deb ... 119s Unpacking r-cran-fansi (1.0.5-1) ... 119s Selecting previously unselected package r-cran-utf8. 119s Preparing to unpack .../304-r-cran-utf8_1.2.4-1_amd64.deb ... 119s Unpacking r-cran-utf8 (1.2.4-1) ... 119s Selecting previously unselected package r-cran-pillar. 119s Preparing to unpack .../305-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 119s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 119s Selecting previously unselected package r-cran-tibble. 120s Preparing to unpack .../306-r-cran-tibble_3.2.1+dfsg-2_amd64.deb ... 120s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 120s Selecting previously unselected package r-cran-withr. 120s Preparing to unpack .../307-r-cran-withr_3.0.0+dfsg-1_all.deb ... 120s Unpacking r-cran-withr (3.0.0+dfsg-1) ... 120s Selecting previously unselected package r-cran-tidyselect. 120s Preparing to unpack .../308-r-cran-tidyselect_1.2.1+dfsg-1_amd64.deb ... 120s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 120s Selecting previously unselected package r-cran-dplyr. 120s Preparing to unpack .../309-r-cran-dplyr_1.1.4-1_amd64.deb ... 120s Unpacking r-cran-dplyr (1.1.4-1) ... 120s Selecting previously unselected package r-cran-purrr. 120s Preparing to unpack .../310-r-cran-purrr_1.0.2-1_amd64.deb ... 120s Unpacking r-cran-purrr (1.0.2-1) ... 120s Selecting previously unselected package r-cran-stringi. 120s Preparing to unpack .../311-r-cran-stringi_1.8.3-1_amd64.deb ... 120s Unpacking r-cran-stringi (1.8.3-1) ... 120s Selecting previously unselected package r-cran-stringr. 120s Preparing to unpack .../312-r-cran-stringr_1.5.1-1_all.deb ... 120s Unpacking r-cran-stringr (1.5.1-1) ... 120s Selecting previously unselected package r-cran-tidyr. 120s Preparing to unpack .../313-r-cran-tidyr_1.3.1-1_amd64.deb ... 120s Unpacking r-cran-tidyr (1.3.1-1) ... 120s Selecting previously unselected package r-cran-dbplyr. 120s Preparing to unpack .../314-r-cran-dbplyr_2.4.0+dfsg-1_all.deb ... 120s Unpacking r-cran-dbplyr (2.4.0+dfsg-1) ... 120s Selecting previously unselected package r-cran-filelock. 120s Preparing to unpack .../315-r-cran-filelock_1.0.3-1_amd64.deb ... 120s Unpacking r-cran-filelock (1.0.3-1) ... 120s Selecting previously unselected package r-bioc-biocfilecache. 120s Preparing to unpack .../316-r-bioc-biocfilecache_2.12.0+dfsg-1_all.deb ... 120s Unpacking r-bioc-biocfilecache (2.12.0+dfsg-1) ... 120s Selecting previously unselected package r-bioc-biocio. 120s Preparing to unpack .../317-r-bioc-biocio_1.14.0+dfsg-1_all.deb ... 120s Unpacking r-bioc-biocio (1.14.0+dfsg-1) ... 120s Selecting previously unselected package r-cran-formatr. 120s Preparing to unpack .../318-r-cran-formatr_1.14-2_all.deb ... 120s Unpacking r-cran-formatr (1.14-2) ... 120s Selecting previously unselected package r-cran-lambda.r. 120s Preparing to unpack .../319-r-cran-lambda.r_1.2.4-2build1_all.deb ... 120s Unpacking r-cran-lambda.r (1.2.4-2build1) ... 120s Selecting previously unselected package r-cran-futile.options. 120s Preparing to unpack .../320-r-cran-futile.options_1.0.1-3build1_all.deb ... 120s Unpacking r-cran-futile.options (1.0.1-3build1) ... 120s Selecting previously unselected package r-cran-futile.logger. 120s Preparing to unpack .../321-r-cran-futile.logger_1.4.3-4build1_all.deb ... 120s Unpacking r-cran-futile.logger (1.4.3-4build1) ... 120s Selecting previously unselected package r-cran-snow. 120s Preparing to unpack .../322-r-cran-snow_1%3a0.4.4-2_all.deb ... 120s Unpacking r-cran-snow (1:0.4.4-2) ... 120s Selecting previously unselected package r-cran-codetools. 120s Preparing to unpack .../323-r-cran-codetools_0.2-20-1_all.deb ... 120s Unpacking r-cran-codetools (0.2-20-1) ... 120s Selecting previously unselected package r-cran-bh. 121s Preparing to unpack .../324-r-cran-bh_1.84.0-1_all.deb ... 121s Unpacking r-cran-bh (1.84.0-1) ... 121s Selecting previously unselected package r-bioc-biocparallel. 121s Preparing to unpack .../325-r-bioc-biocparallel_1.38.0-2_amd64.deb ... 121s Unpacking r-bioc-biocparallel (1.38.0-2) ... 121s Selecting previously unselected package r-cran-base64enc. 121s Preparing to unpack .../326-r-cran-base64enc_0.1-3-3_amd64.deb ... 121s Unpacking r-cran-base64enc (0.1-3-3) ... 121s Selecting previously unselected package r-cran-digest. 121s Preparing to unpack .../327-r-cran-digest_0.6.36-1_amd64.deb ... 121s Unpacking r-cran-digest (0.6.36-1) ... 121s Selecting previously unselected package r-cran-htmltools. 121s Preparing to unpack .../328-r-cran-htmltools_0.5.8.1-1_amd64.deb ... 121s Unpacking r-cran-htmltools (0.5.8.1-1) ... 121s Selecting previously unselected package r-cran-evaluate. 121s Preparing to unpack .../329-r-cran-evaluate_0.24.0-1_all.deb ... 121s Unpacking r-cran-evaluate (0.24.0-1) ... 121s Selecting previously unselected package r-cran-xfun. 121s Preparing to unpack .../330-r-cran-xfun_0.45+dfsg-1_amd64.deb ... 121s Unpacking r-cran-xfun (0.45+dfsg-1) ... 121s Selecting previously unselected package r-cran-highr. 121s Preparing to unpack .../331-r-cran-highr_0.11+dfsg-1_all.deb ... 121s Unpacking r-cran-highr (0.11+dfsg-1) ... 121s Selecting previously unselected package r-cran-yaml. 121s Preparing to unpack .../332-r-cran-yaml_2.3.8-2_amd64.deb ... 121s Unpacking r-cran-yaml (2.3.8-2) ... 121s Selecting previously unselected package libjs-mathjax. 121s Preparing to unpack .../333-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 121s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 122s Selecting previously unselected package r-cran-knitr. 122s Preparing to unpack .../334-r-cran-knitr_1.47+dfsg-1_all.deb ... 122s Unpacking r-cran-knitr (1.47+dfsg-1) ... 122s Selecting previously unselected package r-cran-jquerylib. 122s Preparing to unpack .../335-r-cran-jquerylib_0.1.4+dfsg-4_all.deb ... 122s Unpacking r-cran-jquerylib (0.1.4+dfsg-4) ... 122s Selecting previously unselected package r-cran-fs. 122s Preparing to unpack .../336-r-cran-fs_1.6.4+dfsg-1_amd64.deb ... 122s Unpacking r-cran-fs (1.6.4+dfsg-1) ... 122s Selecting previously unselected package r-cran-rappdirs. 122s Preparing to unpack .../337-r-cran-rappdirs_0.3.3-1_amd64.deb ... 122s Unpacking r-cran-rappdirs (0.3.3-1) ... 122s Selecting previously unselected package r-cran-sass. 122s Preparing to unpack .../338-r-cran-sass_0.4.9+dfsg-1_amd64.deb ... 122s Unpacking r-cran-sass (0.4.9+dfsg-1) ... 122s Selecting previously unselected package r-cran-bslib. 122s Preparing to unpack .../339-r-cran-bslib_0.7.0+dfsg-1_all.deb ... 122s Unpacking r-cran-bslib (0.7.0+dfsg-1) ... 122s Selecting previously unselected package r-cran-fontawesome. 123s Preparing to unpack .../340-r-cran-fontawesome_0.5.2-1_all.deb ... 123s Unpacking r-cran-fontawesome (0.5.2-1) ... 123s Selecting previously unselected package r-cran-tinytex. 123s Preparing to unpack .../341-r-cran-tinytex_0.51-1_all.deb ... 123s Unpacking r-cran-tinytex (0.51-1) ... 123s Selecting previously unselected package libjs-modernizr. 123s Preparing to unpack .../342-libjs-modernizr_3.13.0-0.1_all.deb ... 123s Unpacking libjs-modernizr (3.13.0-0.1) ... 123s Selecting previously unselected package r-cran-pkgkitten. 123s Preparing to unpack .../343-r-cran-pkgkitten_0.2.4-1_all.deb ... 123s Unpacking r-cran-pkgkitten (0.2.4-1) ... 123s Selecting previously unselected package r-cran-rcpp. 123s Preparing to unpack .../344-r-cran-rcpp_1.0.13-1_amd64.deb ... 123s Unpacking r-cran-rcpp (1.0.13-1) ... 123s Selecting previously unselected package r-cran-later. 123s Preparing to unpack .../345-r-cran-later_1.3.2+dfsg-1_amd64.deb ... 123s Unpacking r-cran-later (1.3.2+dfsg-1) ... 123s Selecting previously unselected package r-cran-promises. 123s Preparing to unpack .../346-r-cran-promises_1.3.0+dfsg-1_amd64.deb ... 123s Unpacking r-cran-promises (1.3.0+dfsg-1) ... 123s Selecting previously unselected package r-cran-httpuv. 123s Preparing to unpack .../347-r-cran-httpuv_1.6.15+dfsg-1_amd64.deb ... 123s Unpacking r-cran-httpuv (1.6.15+dfsg-1) ... 123s Selecting previously unselected package r-cran-sourcetools. 123s Preparing to unpack .../348-r-cran-sourcetools_0.1.7-1-1_amd64.deb ... 123s Unpacking r-cran-sourcetools (0.1.7-1-1) ... 123s Selecting previously unselected package r-cran-commonmark. 123s Preparing to unpack .../349-r-cran-commonmark_1.9.1-1_amd64.deb ... 123s Unpacking r-cran-commonmark (1.9.1-1) ... 123s Selecting previously unselected package libjs-twitter-bootstrap-datepicker. 123s Preparing to unpack .../350-libjs-twitter-bootstrap-datepicker_1.3.1+dfsg1-4.1_all.deb ... 123s Unpacking libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... 123s Selecting previously unselected package r-cran-shiny. 123s Preparing to unpack .../351-r-cran-shiny_1.8.1.1+dfsg-1_all.deb ... 123s Unpacking r-cran-shiny (1.8.1.1+dfsg-1) ... 123s Selecting previously unselected package r-cran-rmarkdown. 123s Preparing to unpack .../352-r-cran-rmarkdown_2.27+dfsg-1_all.deb ... 123s Unpacking r-cran-rmarkdown (2.27+dfsg-1) ... 124s Selecting previously unselected package r-cran-bookdown. 124s Preparing to unpack .../353-r-cran-bookdown_0.40+dfsg-1_all.deb ... 124s Unpacking r-cran-bookdown (0.40+dfsg-1) ... 124s Selecting previously unselected package r-cran-biocmanager. 124s Preparing to unpack .../354-r-cran-biocmanager_1.30.22+dfsg-2_all.deb ... 124s Unpacking r-cran-biocmanager (1.30.22+dfsg-2) ... 124s Selecting previously unselected package tex-common. 124s Preparing to unpack .../355-tex-common_6.18_all.deb ... 124s Unpacking tex-common (6.18) ... 124s Selecting previously unselected package t1utils. 124s Preparing to unpack .../356-t1utils_1.41-4build3_amd64.deb ... 124s Unpacking t1utils (1.41-4build3) ... 124s Selecting previously unselected package texlive-binaries. 124s Preparing to unpack .../357-texlive-binaries_2024.20240313.70630+ds-4_amd64.deb ... 124s Unpacking texlive-binaries (2024.20240313.70630+ds-4) ... 124s Selecting previously unselected package texlive-base. 124s Preparing to unpack .../358-texlive-base_2024.20240706-1_all.deb ... 124s Unpacking texlive-base (2024.20240706-1) ... 125s Selecting previously unselected package texlive-latex-base. 125s Preparing to unpack .../359-texlive-latex-base_2024.20240706-1_all.deb ... 125s Unpacking texlive-latex-base (2024.20240706-1) ... 126s Selecting previously unselected package texlive-bibtex-extra. 126s Preparing to unpack .../360-texlive-bibtex-extra_2024.20240706-2_all.deb ... 126s Unpacking texlive-bibtex-extra (2024.20240706-2) ... 129s Selecting previously unselected package r-bioc-biocversion. 129s Preparing to unpack .../361-r-bioc-biocversion_3.19.1-1_all.deb ... 129s Unpacking r-bioc-biocversion (3.19.1-1) ... 129s Selecting previously unselected package r-bioc-biocstyle. 129s Preparing to unpack .../362-r-bioc-biocstyle_2.32.1+dfsg-1_all.deb ... 129s Unpacking r-bioc-biocstyle (2.32.1+dfsg-1) ... 129s Selecting previously unselected package r-cran-hms. 129s Preparing to unpack .../363-r-cran-hms_1.1.3-1_all.deb ... 129s Unpacking r-cran-hms (1.1.3-1) ... 129s Selecting previously unselected package r-cran-prettyunits. 129s Preparing to unpack .../364-r-cran-prettyunits_1.2.0-1_all.deb ... 129s Unpacking r-cran-prettyunits (1.2.0-1) ... 129s Selecting previously unselected package r-cran-progress. 129s Preparing to unpack .../365-r-cran-progress_1.2.3-1_all.deb ... 129s Unpacking r-cran-progress (1.2.3-1) ... 129s Selecting previously unselected package r-cran-httr2. 129s Preparing to unpack .../366-r-cran-httr2_1.0.2-1_all.deb ... 129s Unpacking r-cran-httr2 (1.0.2-1) ... 129s Selecting previously unselected package r-cran-xml2. 129s Preparing to unpack .../367-r-cran-xml2_1.3.6-1_amd64.deb ... 129s Unpacking r-cran-xml2 (1.3.6-1) ... 129s Selecting previously unselected package r-bioc-biomart. 129s Preparing to unpack .../368-r-bioc-biomart_2.60.1+dfsg-1_all.deb ... 129s Unpacking r-bioc-biomart (2.60.1+dfsg-1) ... 129s Selecting previously unselected package r-cran-lattice. 129s Preparing to unpack .../369-r-cran-lattice_0.22-6-1_amd64.deb ... 129s Unpacking r-cran-lattice (0.22-6-1) ... 129s Selecting previously unselected package r-cran-matrix. 129s Preparing to unpack .../370-r-cran-matrix_1.7-0-3_amd64.deb ... 129s Unpacking r-cran-matrix (1.7-0-3) ... 129s Selecting previously unselected package r-cran-matrixstats. 129s Preparing to unpack .../371-r-cran-matrixstats_1.3.0-1_amd64.deb ... 129s Unpacking r-cran-matrixstats (1.3.0-1) ... 129s Selecting previously unselected package r-bioc-matrixgenerics. 129s Preparing to unpack .../372-r-bioc-matrixgenerics_1.16.0-2_all.deb ... 129s Unpacking r-bioc-matrixgenerics (1.16.0-2) ... 129s Selecting previously unselected package r-cran-abind. 129s Preparing to unpack .../373-r-cran-abind_1.4-5-2_all.deb ... 129s Unpacking r-cran-abind (1.4-5-2) ... 130s Selecting previously unselected package r-bioc-s4arrays. 130s Preparing to unpack .../374-r-bioc-s4arrays_1.4.1+dfsg-1_amd64.deb ... 130s Unpacking r-bioc-s4arrays (1.4.1+dfsg-1) ... 130s Selecting previously unselected package r-bioc-sparsearray. 130s Preparing to unpack .../375-r-bioc-sparsearray_1.4.8+dfsg-1_amd64.deb ... 130s Unpacking r-bioc-sparsearray (1.4.8+dfsg-1) ... 130s Selecting previously unselected package r-bioc-delayedarray. 130s Preparing to unpack .../376-r-bioc-delayedarray_0.30.1+dfsg-1_amd64.deb ... 130s Unpacking r-bioc-delayedarray (0.30.1+dfsg-1) ... 130s Selecting previously unselected package r-bioc-genomicranges. 130s Preparing to unpack .../377-r-bioc-genomicranges_1.56.1+dfsg-1_amd64.deb ... 130s Unpacking r-bioc-genomicranges (1.56.1+dfsg-1) ... 130s Selecting previously unselected package r-bioc-summarizedexperiment. 130s Preparing to unpack .../378-r-bioc-summarizedexperiment_1.34.0+dfsg-1_all.deb ... 130s Unpacking r-bioc-summarizedexperiment (1.34.0+dfsg-1) ... 130s Selecting previously unselected package r-cran-locfit. 130s Preparing to unpack .../379-r-cran-locfit_1.5-9.9-1_amd64.deb ... 130s Unpacking r-cran-locfit (1.5-9.9-1) ... 130s Selecting previously unselected package r-cran-gtable. 130s Preparing to unpack .../380-r-cran-gtable_0.3.5+dfsg-1_all.deb ... 130s Unpacking r-cran-gtable (0.3.5+dfsg-1) ... 130s Selecting previously unselected package r-cran-isoband. 130s Preparing to unpack .../381-r-cran-isoband_0.2.7-1_amd64.deb ... 130s Unpacking r-cran-isoband (0.2.7-1) ... 130s Selecting previously unselected package r-cran-mass. 130s Preparing to unpack .../382-r-cran-mass_7.3-61-1_amd64.deb ... 130s Unpacking r-cran-mass (7.3-61-1) ... 130s Selecting previously unselected package r-cran-nlme. 130s Preparing to unpack .../383-r-cran-nlme_3.1.166-1_amd64.deb ... 130s Unpacking r-cran-nlme (3.1.166-1) ... 130s Selecting previously unselected package r-cran-mgcv. 130s Preparing to unpack .../384-r-cran-mgcv_1.9-1-1_amd64.deb ... 130s Unpacking r-cran-mgcv (1.9-1-1) ... 130s Selecting previously unselected package r-cran-farver. 130s Preparing to unpack .../385-r-cran-farver_2.1.2-1_amd64.deb ... 130s Unpacking r-cran-farver (2.1.2-1) ... 130s Selecting previously unselected package r-cran-labeling. 130s Preparing to unpack .../386-r-cran-labeling_0.4.3-1_all.deb ... 130s Unpacking r-cran-labeling (0.4.3-1) ... 130s Selecting previously unselected package r-cran-colorspace. 130s Preparing to unpack .../387-r-cran-colorspace_2.1-0+dfsg-1_amd64.deb ... 130s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ... 131s Selecting previously unselected package r-cran-munsell. 131s Preparing to unpack .../388-r-cran-munsell_0.5.1-1_all.deb ... 131s Unpacking r-cran-munsell (0.5.1-1) ... 131s Selecting previously unselected package r-cran-rcolorbrewer. 131s Preparing to unpack .../389-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 131s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 131s Selecting previously unselected package r-cran-viridislite. 131s Preparing to unpack .../390-r-cran-viridislite_0.4.2-2_all.deb ... 131s Unpacking r-cran-viridislite (0.4.2-2) ... 131s Selecting previously unselected package r-cran-scales. 131s Preparing to unpack .../391-r-cran-scales_1.3.0-1_all.deb ... 131s Unpacking r-cran-scales (1.3.0-1) ... 131s Selecting previously unselected package r-cran-ggplot2. 131s Preparing to unpack .../392-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 131s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 131s Selecting previously unselected package r-cran-rcpparmadillo. 131s Preparing to unpack .../393-r-cran-rcpparmadillo_14.0.0-1-1_amd64.deb ... 131s Unpacking r-cran-rcpparmadillo (14.0.0-1-1) ... 131s Selecting previously unselected package r-bioc-deseq2. 131s Preparing to unpack .../394-r-bioc-deseq2_1.44.0+dfsg-1_amd64.deb ... 131s Unpacking r-bioc-deseq2 (1.44.0+dfsg-1) ... 131s Selecting previously unselected package r-cran-hwriter. 131s Preparing to unpack .../395-r-cran-hwriter_1.3.2.1-1_all.deb ... 131s Unpacking r-cran-hwriter (1.3.2.1-1) ... 131s Selecting previously unselected package r-cran-bitops. 131s Preparing to unpack .../396-r-cran-bitops_1.0-7-1_amd64.deb ... 131s Unpacking r-cran-bitops (1.0-7-1) ... 131s Selecting previously unselected package r-bioc-rhtslib. 131s Preparing to unpack .../397-r-bioc-rhtslib_3.0.0+dfsg-1_amd64.deb ... 131s Unpacking r-bioc-rhtslib (3.0.0+dfsg-1) ... 131s Selecting previously unselected package r-bioc-rsamtools. 131s Preparing to unpack .../398-r-bioc-rsamtools_2.20.0+dfsg-1_amd64.deb ... 131s Unpacking r-bioc-rsamtools (2.20.0+dfsg-1) ... 132s Selecting previously unselected package r-cran-statmod. 132s Preparing to unpack .../399-r-cran-statmod_1.5.0-1_amd64.deb ... 132s Unpacking r-cran-statmod (1.5.0-1) ... 132s Selecting previously unselected package r-bioc-geneplotter. 132s Preparing to unpack .../400-r-bioc-geneplotter_1.82.0+dfsg-1_all.deb ... 132s Unpacking r-bioc-geneplotter (1.82.0+dfsg-1) ... 132s Selecting previously unselected package r-cran-survival. 132s Preparing to unpack .../401-r-cran-survival_3.7-0-1_amd64.deb ... 132s Unpacking r-cran-survival (3.7-0-1) ... 132s Selecting previously unselected package r-bioc-genefilter. 132s Preparing to unpack .../402-r-bioc-genefilter_1.86.0-1_amd64.deb ... 132s Unpacking r-bioc-genefilter (1.86.0-1) ... 132s Selecting previously unselected package r-bioc-dexseq. 132s Preparing to unpack .../403-r-bioc-dexseq_1.50.0+dfsg-1_all.deb ... 132s Unpacking r-bioc-dexseq (1.50.0+dfsg-1) ... 132s Selecting previously unselected package r-bioc-limma. 132s Preparing to unpack .../404-r-bioc-limma_3.60.4+dfsg-1_amd64.deb ... 132s Unpacking r-bioc-limma (3.60.4+dfsg-1) ... 132s Selecting previously unselected package r-bioc-edger. 132s Preparing to unpack .../405-r-bioc-edger_4.2.1+dfsg-1_amd64.deb ... 132s Unpacking r-bioc-edger (4.2.1+dfsg-1) ... 132s Selecting previously unselected package r-bioc-genomicalignments. 132s Preparing to unpack .../406-r-bioc-genomicalignments_1.40.0-1_amd64.deb ... 132s Unpacking r-bioc-genomicalignments (1.40.0-1) ... 132s Selecting previously unselected package r-cran-rcurl. 132s Preparing to unpack .../407-r-cran-rcurl_1.98-1.14+dfsg-1build2_amd64.deb ... 132s Unpacking r-cran-rcurl (1.98-1.14+dfsg-1build2) ... 132s Selecting previously unselected package r-cran-rjson. 132s Preparing to unpack .../408-r-cran-rjson_0.2.21-1_amd64.deb ... 132s Unpacking r-cran-rjson (0.2.21-1) ... 132s Selecting previously unselected package r-cran-restfulr. 132s Preparing to unpack .../409-r-cran-restfulr_0.0.15-1_amd64.deb ... 132s Unpacking r-cran-restfulr (0.0.15-1) ... 132s Selecting previously unselected package r-bioc-rtracklayer. 132s Preparing to unpack .../410-r-bioc-rtracklayer_1.64.0-1_amd64.deb ... 132s Unpacking r-bioc-rtracklayer (1.64.0-1) ... 132s Selecting previously unselected package r-bioc-genomicfeatures. 132s Preparing to unpack .../411-r-bioc-genomicfeatures_1.56.0+dfsg-1_all.deb ... 132s Unpacking r-bioc-genomicfeatures (1.56.0+dfsg-1) ... 132s Selecting previously unselected package r-bioc-txdbmaker. 133s Preparing to unpack .../412-r-bioc-txdbmaker_1.0.1+ds-1_all.deb ... 133s Unpacking r-bioc-txdbmaker (1.0.1+ds-1) ... 133s Selecting previously unselected package r-bioc-genelendatabase. 133s Preparing to unpack .../413-r-bioc-genelendatabase_1.40.1-1_all.deb ... 133s Unpacking r-bioc-genelendatabase (1.40.1-1) ... 133s Selecting previously unselected package r-bioc-go.db. 133s Preparing to unpack .../414-r-bioc-go.db_3.19.1-1_all.deb ... 133s Unpacking r-bioc-go.db (3.19.1-1) ... 134s Selecting previously unselected package r-cran-biasedurn. 134s Preparing to unpack .../415-r-cran-biasedurn_2.0.11-1_amd64.deb ... 134s Unpacking r-cran-biasedurn (2.0.11-1) ... 134s Selecting previously unselected package r-bioc-goseq. 134s Preparing to unpack .../416-r-bioc-goseq_1.56.0-1_all.deb ... 134s Unpacking r-bioc-goseq (1.56.0-1) ... 134s Selecting previously unselected package r-cran-plyr. 134s Preparing to unpack .../417-r-cran-plyr_1.8.9-1_amd64.deb ... 134s Unpacking r-cran-plyr (1.8.9-1) ... 134s Selecting previously unselected package r-cran-reshape2. 134s Preparing to unpack .../418-r-cran-reshape2_1.4.4-2build1_amd64.deb ... 134s Unpacking r-cran-reshape2 (1.4.4-2build1) ... 134s Selecting previously unselected package r-bioc-qvalue. 134s Preparing to unpack .../419-r-bioc-qvalue_2.36.0-1_all.deb ... 134s Unpacking r-bioc-qvalue (2.36.0-1) ... 134s Selecting previously unselected package r-cran-findpython. 134s Preparing to unpack .../420-r-cran-findpython_1.0.8-1_all.deb ... 134s Unpacking r-cran-findpython (1.0.8-1) ... 134s Selecting previously unselected package r-cran-argparse. 134s Preparing to unpack .../421-r-cran-argparse_2.2.3+dfsg-1_all.deb ... 134s Unpacking r-cran-argparse (2.2.3+dfsg-1) ... 134s Selecting previously unselected package r-cran-backports. 134s Preparing to unpack .../422-r-cran-backports_1.5.0-2_amd64.deb ... 134s Unpacking r-cran-backports (1.5.0-2) ... 134s Selecting previously unselected package r-cran-broom. 134s Preparing to unpack .../423-r-cran-broom_1.0.6+dfsg-1_all.deb ... 134s Unpacking r-cran-broom (1.0.6+dfsg-1) ... 134s Selecting previously unselected package r-cran-ps. 134s Preparing to unpack .../424-r-cran-ps_1.7.6-1_amd64.deb ... 134s Unpacking r-cran-ps (1.7.6-1) ... 134s Selecting previously unselected package r-cran-processx. 134s Preparing to unpack .../425-r-cran-processx_3.8.4-1_amd64.deb ... 134s Unpacking r-cran-processx (3.8.4-1) ... 134s Selecting previously unselected package r-cran-callr. 134s Preparing to unpack .../426-r-cran-callr_3.7.6-1_all.deb ... 134s Unpacking r-cran-callr (3.7.6-1) ... 135s Selecting previously unselected package r-cran-rematch. 135s Preparing to unpack .../427-r-cran-rematch_2.0.0-1_all.deb ... 135s Unpacking r-cran-rematch (2.0.0-1) ... 135s Selecting previously unselected package r-cran-cellranger. 135s Preparing to unpack .../428-r-cran-cellranger_1.1.0-3_all.deb ... 135s Unpacking r-cran-cellranger (1.1.0-3) ... 135s Selecting previously unselected package r-cran-clipr. 135s Preparing to unpack .../429-r-cran-clipr_0.8.0-1_all.deb ... 135s Unpacking r-cran-clipr (0.8.0-1) ... 135s Selecting previously unselected package r-cran-cluster. 135s Preparing to unpack .../430-r-cran-cluster_2.1.6-1build1_amd64.deb ... 135s Unpacking r-cran-cluster (2.1.6-1build1) ... 135s Selecting previously unselected package r-cran-conflicted. 135s Preparing to unpack .../431-r-cran-conflicted_1.2.0-1.1_all.deb ... 135s Unpacking r-cran-conflicted (1.2.0-1.1) ... 135s Selecting previously unselected package r-cran-data.table. 135s Preparing to unpack .../432-r-cran-data.table_1.15.4+dfsg-2.2_amd64.deb ... 135s Unpacking r-cran-data.table (1.15.4+dfsg-2.2) ... 135s Selecting previously unselected package r-cran-dtplyr. 135s Preparing to unpack .../433-r-cran-dtplyr_1.3.1-1_all.deb ... 135s Unpacking r-cran-dtplyr (1.3.1-1) ... 135s Selecting previously unselected package r-cran-ellipsis. 135s Preparing to unpack .../434-r-cran-ellipsis_0.3.2-2_amd64.deb ... 135s Unpacking r-cran-ellipsis (0.3.2-2) ... 135s Selecting previously unselected package r-cran-fastcluster. 135s Preparing to unpack .../435-r-cran-fastcluster_1.2.6-1build1_amd64.deb ... 135s Unpacking r-cran-fastcluster (1.2.6-1build1) ... 135s Selecting previously unselected package r-cran-forcats. 135s Preparing to unpack .../436-r-cran-forcats_1.0.0-1_all.deb ... 135s Unpacking r-cran-forcats (1.0.0-1) ... 135s Selecting previously unselected package r-cran-gargle. 135s Preparing to unpack .../437-r-cran-gargle_1.5.2-1_all.deb ... 135s Unpacking r-cran-gargle (1.5.2-1) ... 135s Selecting previously unselected package r-cran-ggdendro. 135s Preparing to unpack .../438-r-cran-ggdendro_0.2.0+dfsg-1_all.deb ... 135s Unpacking r-cran-ggdendro (0.2.0+dfsg-1) ... 135s Selecting previously unselected package r-cran-uuid. 135s Preparing to unpack .../439-r-cran-uuid_1.2-1-1_amd64.deb ... 135s Unpacking r-cran-uuid (1.2-1-1) ... 135s Selecting previously unselected package r-cran-googledrive. 135s Preparing to unpack .../440-r-cran-googledrive_2.1.1-1_all.deb ... 135s Unpacking r-cran-googledrive (2.1.1-1) ... 135s Selecting previously unselected package r-cran-ids. 135s Preparing to unpack .../441-r-cran-ids_1.0.1-2_all.deb ... 135s Unpacking r-cran-ids (1.0.1-2) ... 135s Selecting previously unselected package r-cran-rematch2. 135s Preparing to unpack .../442-r-cran-rematch2_2.1.2-2build1_all.deb ... 135s Unpacking r-cran-rematch2 (2.1.2-2build1) ... 136s Selecting previously unselected package r-cran-googlesheets4. 136s Preparing to unpack .../443-r-cran-googlesheets4_1.1.1-1_all.deb ... 136s Unpacking r-cran-googlesheets4 (1.1.1-1) ... 136s Selecting previously unselected package r-cran-gridextra. 136s Preparing to unpack .../444-r-cran-gridextra_2.3-3build1_all.deb ... 136s Unpacking r-cran-gridextra (2.3-3build1) ... 136s Selecting previously unselected package r-cran-goplot. 136s Preparing to unpack .../445-r-cran-goplot_1.0.2-2_all.deb ... 136s Unpacking r-cran-goplot (1.0.2-2) ... 136s Selecting previously unselected package r-cran-tzdb. 136s Preparing to unpack .../446-r-cran-tzdb_0.4.0-2_amd64.deb ... 136s Unpacking r-cran-tzdb (0.4.0-2) ... 136s Selecting previously unselected package r-cran-vroom. 136s Preparing to unpack .../447-r-cran-vroom_1.6.5-1_amd64.deb ... 136s Unpacking r-cran-vroom (1.6.5-1) ... 136s Selecting previously unselected package r-cran-readr. 136s Preparing to unpack .../448-r-cran-readr_2.1.5-1_amd64.deb ... 136s Unpacking r-cran-readr (2.1.5-1) ... 136s Selecting previously unselected package r-cran-haven. 136s Preparing to unpack .../449-r-cran-haven_2.5.4-1_amd64.deb ... 136s Unpacking r-cran-haven (2.5.4-1) ... 136s Selecting previously unselected package r-cran-kernsmooth. 136s Preparing to unpack .../450-r-cran-kernsmooth_2.23-24-1_amd64.deb ... 136s Unpacking r-cran-kernsmooth (2.23-24-1) ... 136s Selecting previously unselected package r-cran-timechange. 136s Preparing to unpack .../451-r-cran-timechange_0.3.0-1_amd64.deb ... 136s Unpacking r-cran-timechange (0.3.0-1) ... 136s Selecting previously unselected package r-cran-lubridate. 136s Preparing to unpack .../452-r-cran-lubridate_1.9.3+dfsg-1_amd64.deb ... 136s Unpacking r-cran-lubridate (1.9.3+dfsg-1) ... 136s Selecting previously unselected package r-cran-modelr. 136s Preparing to unpack .../453-r-cran-modelr_0.1.11-1_all.deb ... 136s Unpacking r-cran-modelr (0.1.11-1) ... 136s Selecting previously unselected package r-cran-systemfonts. 136s Preparing to unpack .../454-r-cran-systemfonts_1.1.0-1_amd64.deb ... 136s Unpacking r-cran-systemfonts (1.1.0-1) ... 136s Selecting previously unselected package r-cran-textshaping. 136s Preparing to unpack .../455-r-cran-textshaping_0.3.7-2_amd64.deb ... 136s Unpacking r-cran-textshaping (0.3.7-2) ... 136s Selecting previously unselected package r-cran-ragg. 136s Preparing to unpack .../456-r-cran-ragg_1.3.2-1_amd64.deb ... 136s Unpacking r-cran-ragg (1.3.2-1) ... 137s Selecting previously unselected package r-cran-readxl. 137s Preparing to unpack .../457-r-cran-readxl_1.4.3-1_amd64.deb ... 137s Unpacking r-cran-readxl (1.4.3-1) ... 137s Selecting previously unselected package r-cran-rstudioapi. 137s Preparing to unpack .../458-r-cran-rstudioapi_0.16.0-1_all.deb ... 137s Unpacking r-cran-rstudioapi (0.16.0-1) ... 137s Selecting previously unselected package r-cran-reprex. 137s Preparing to unpack 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unpack .../465-rsem_1.3.3+dfsg-3build1_amd64.deb ... 137s Unpacking rsem (1.3.3+dfsg-3build1) ... 137s Selecting previously unselected package salmon. 137s Preparing to unpack .../466-salmon_1.10.2+ds1-1build2_amd64.deb ... 137s Unpacking salmon (1.10.2+ds1-1build2) ... 138s Selecting previously unselected package samtools. 138s Preparing to unpack .../467-samtools_1.20-3_amd64.deb ... 138s Unpacking samtools (1.20-3) ... 138s Selecting previously unselected package subread. 138s Preparing to unpack .../468-subread_2.0.6+dfsg-3_amd64.deb ... 138s Unpacking subread (2.0.6+dfsg-3) ... 138s Selecting previously unselected package libjbzip2-java. 138s Preparing to unpack .../469-libjbzip2-java_0.9.1-8_all.deb ... 138s Unpacking libjbzip2-java (0.9.1-8) ... 138s Selecting previously unselected package trimmomatic. 138s Preparing to unpack .../470-trimmomatic_0.39+dfsg-2_all.deb ... 138s Unpacking trimmomatic (0.39+dfsg-2) ... 138s Selecting previously unselected package trinityrnaseq. 138s 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Setting up adwaita-icon-theme (47.0-1) ... 151s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 151s Setting up liblwp-protocol-https-perl (6.14-1) ... 151s Setting up liberror-prone-java (2.18.0-1) ... 151s Setting up libwww-perl (6.77-1) ... 151s Setting up humanity-icon-theme (0.6.16) ... 151s Setting up libguava-java (32.0.1-1) ... 151s Setting up ubuntu-mono (24.04-0ubuntu1) ... 151s Setting up libjung-free-java (2.1.1-2) ... 151s Processing triggers for libglib2.0-0t64:amd64 (2.82.1-0ubuntu1) ... 151s Setting up libgtk-3-0t64:amd64 (3.24.43-3ubuntu2) ... 151s Processing triggers for install-info (7.1.1-1) ... 151s Processing triggers for libc-bin (2.40-1ubuntu3) ... 152s Processing triggers for man-db (2.12.1-3) ... 154s Processing triggers for ca-certificates-java (20240118) ... 154s Adding debian:ACCVRAIZ1.pem 154s Adding debian:AC_RAIZ_FNMT-RCM.pem 154s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 154s Adding debian:ANF_Secure_Server_Root_CA.pem 154s Adding debian:Actalis_Authentication_Root_CA.pem 154s Adding debian:AffirmTrust_Commercial.pem 154s Adding debian:AffirmTrust_Networking.pem 154s Adding debian:AffirmTrust_Premium.pem 154s Adding debian:AffirmTrust_Premium_ECC.pem 154s Adding debian:Amazon_Root_CA_1.pem 154s Adding debian:Amazon_Root_CA_2.pem 154s Adding debian:Amazon_Root_CA_3.pem 154s Adding debian:Amazon_Root_CA_4.pem 154s Adding debian:Atos_TrustedRoot_2011.pem 154s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 154s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 154s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 154s Adding debian:BJCA_Global_Root_CA1.pem 154s Adding debian:BJCA_Global_Root_CA2.pem 154s Adding debian:Baltimore_CyberTrust_Root.pem 154s Adding debian:Buypass_Class_2_Root_CA.pem 154s Adding debian:Buypass_Class_3_Root_CA.pem 154s Adding debian:CA_Disig_Root_R2.pem 154s Adding debian:CFCA_EV_ROOT.pem 154s Adding debian:COMODO_Certification_Authority.pem 154s Adding debian:COMODO_ECC_Certification_Authority.pem 154s Adding debian:COMODO_RSA_Certification_Authority.pem 154s Adding debian:Certainly_Root_E1.pem 154s Adding debian:Certainly_Root_R1.pem 154s Adding debian:Certigna.pem 154s Adding debian:Certigna_Root_CA.pem 154s Adding debian:Certum_EC-384_CA.pem 154s Adding debian:Certum_Trusted_Network_CA.pem 154s Adding debian:Certum_Trusted_Network_CA_2.pem 154s Adding debian:Certum_Trusted_Root_CA.pem 154s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 154s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 155s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 155s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 155s Adding debian:Comodo_AAA_Services_root.pem 155s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 155s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 155s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 155s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 155s Adding debian:DigiCert_Assured_ID_Root_CA.pem 155s Adding debian:DigiCert_Assured_ID_Root_G2.pem 155s Adding debian:DigiCert_Assured_ID_Root_G3.pem 155s Adding debian:DigiCert_Global_Root_CA.pem 155s Adding debian:DigiCert_Global_Root_G2.pem 155s Adding debian:DigiCert_Global_Root_G3.pem 155s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 155s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 155s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 155s Adding debian:DigiCert_Trusted_Root_G4.pem 155s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 155s Adding debian:Entrust_Root_Certification_Authority.pem 155s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 155s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 155s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 155s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 155s Adding debian:GLOBALTRUST_2020.pem 155s Adding debian:GTS_Root_R1.pem 155s Adding debian:GTS_Root_R2.pem 155s Adding debian:GTS_Root_R3.pem 155s Adding debian:GTS_Root_R4.pem 155s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 155s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 155s Adding debian:GlobalSign_Root_CA.pem 155s Adding debian:GlobalSign_Root_CA_-_R3.pem 155s Adding debian:GlobalSign_Root_CA_-_R6.pem 155s Adding debian:GlobalSign_Root_E46.pem 155s Adding debian:GlobalSign_Root_R46.pem 155s Adding debian:Go_Daddy_Class_2_CA.pem 155s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 155s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 155s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 155s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 155s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 155s Adding debian:HiPKI_Root_CA_-_G1.pem 155s Adding debian:Hongkong_Post_Root_CA_3.pem 155s Adding debian:ISRG_Root_X1.pem 155s Adding debian:ISRG_Root_X2.pem 155s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 155s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 155s Adding debian:Izenpe.com.pem 155s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 155s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 155s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 155s Adding debian:NAVER_Global_Root_Certification_Authority.pem 155s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 155s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 155s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 155s Adding debian:QuoVadis_Root_CA_1_G3.pem 155s Adding debian:QuoVadis_Root_CA_2.pem 155s Adding debian:QuoVadis_Root_CA_2_G3.pem 155s Adding debian:QuoVadis_Root_CA_3.pem 155s Adding debian:QuoVadis_Root_CA_3_G3.pem 155s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 155s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 155s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 155s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 155s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 155s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 155s Adding debian:SZAFIR_ROOT_CA2.pem 155s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 155s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 155s Adding debian:SecureSign_RootCA11.pem 155s Adding debian:SecureTrust_CA.pem 155s Adding debian:Secure_Global_CA.pem 155s Adding debian:Security_Communication_ECC_RootCA1.pem 155s Adding debian:Security_Communication_RootCA2.pem 155s Adding debian:Security_Communication_RootCA3.pem 155s Adding debian:Security_Communication_Root_CA.pem 155s Adding debian:Starfield_Class_2_CA.pem 155s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 155s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 155s Adding debian:SwissSign_Gold_CA_-_G2.pem 155s Adding debian:SwissSign_Silver_CA_-_G2.pem 155s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 155s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 155s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 155s Adding debian:TWCA_Global_Root_CA.pem 155s Adding debian:TWCA_Root_Certification_Authority.pem 155s Adding debian:TeliaSonera_Root_CA_v1.pem 155s Adding debian:Telia_Root_CA_v2.pem 155s Adding debian:TrustAsia_Global_Root_CA_G3.pem 155s Adding debian:TrustAsia_Global_Root_CA_G4.pem 155s Adding debian:Trustwave_Global_Certification_Authority.pem 155s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 155s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 155s Adding debian:TunTrust_Root_CA.pem 155s Adding debian:UCA_Extended_Validation_Root.pem 155s Adding debian:UCA_Global_G2_Root.pem 155s Adding debian:USERTrust_ECC_Certification_Authority.pem 155s Adding debian:USERTrust_RSA_Certification_Authority.pem 155s Adding debian:XRamp_Global_CA_Root.pem 155s Adding debian:certSIGN_ROOT_CA.pem 155s Adding debian:certSIGN_Root_CA_G2.pem 155s Adding debian:e-Szigno_Root_CA_2017.pem 155s Adding debian:ePKI_Root_Certification_Authority.pem 155s Adding debian:emSign_ECC_Root_CA_-_C3.pem 155s Adding debian:emSign_ECC_Root_CA_-_G3.pem 155s Adding debian:emSign_Root_CA_-_C1.pem 155s Adding debian:emSign_Root_CA_-_G1.pem 155s Adding debian:vTrus_ECC_Root_CA.pem 155s Adding debian:vTrus_Root_CA.pem 155s done. 155s Setting up default-jre-headless (2:1.21-76) ... 155s Setting up jaligner (1.0+dfsg-11) ... 155s Setting up openjdk-21-jre:amd64 (21.0.5+11-1) ... 155s Setting up default-jre (2:1.21-76) ... 155s Setting up trimmomatic (0.39+dfsg-2) ... 155s Setting up trinityrnaseq (2.15.1+dfsg-5build1) ... 155s Setting up autopkgtest-satdep (0) ... 155s Processing triggers for tex-common (6.18) ... 156s Running updmap-sys. This may take some time... done. 156s Running mktexlsr /var/lib/texmf ... done. 156s Building format(s) --all. 194s This may take some time... done. 217s (Reading database ... 147395 files and directories currently installed.) 217s Removing autopkgtest-satdep (0) ... 217s autopkgtest [17:40:33]: test run-tests: [----------------------- 218s cd test_Trinity_Assembly && make test_all 218s make[1]: Entering directory '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly' 218s ./runMe.sh 218s #!/bin/bash -ve 218s 218s ####################################################### 218s ## Run Trinity to Generate Transcriptome Assemblies ## 218s ####################################################### 218s 218s if [ -z ${TRINITY_HOME} ]; then 218s echo "Must set env var TRINITY_HOME" 218s exit 1 218s fi 218s 218s 218s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \ 218s --left reads.left.fq.gz \ 218s --right reads.right.fq.gz \ 218s --SS_lib_type RF \ 218s --CPU 1 \ 218s --no_cleanup 218s 218s 218s ______ ____ ____ ____ ____ ______ __ __ 218s | || \ | || \ | || || | | 218s | || D ) | | | _ | | | | || | | 218s |_| |_|| / | | | | | | | |_| |_|| ~ | 218s | | | \ | | | | | | | | | |___, | 218s | | | . \ | | | | | | | | | | | 218s |__| |__|\_||____||__|__||____| |__| |____/ 218s 218s Trinity-v2.15.1 218s 218s 218s 218s Left read files: $VAR1 = [ 218s 'reads.left.fq.gz' 218s ]; 218s Right read files: $VAR1 = [ 218s 'reads.right.fq.gz' 218s ]; 218s Saturday, November 2, 2024: 17:40:34 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir 218s Saturday, November 2, 2024: 17:40:34 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis 218s 218s 218s ---------------------------------------------------------------------------------- 218s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 218s ---------------------------------------------------------------------------------- 218s 218s --------------------------------------------------------------- 218s ------------ In silico Read Normalization --------------------- 218s -- (Removing Excess Reads Beyond 200 Coverage -- 218s --------------------------------------------------------------- 218s 218s # running normalization on reads: $VAR1 = [ 218s [ 218s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz' 218s ], 218s [ 218s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz' 218s ] 218s ]; 218s 218s 218s Saturday, November 2, 2024: 17:40:34 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G --max_cov 200 --min_cov 1 --CPU 1 --output /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization --max_CV 10000 --SS_lib_type RF --no_cleanup --left /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together --PARALLEL_STATS 218s -prepping seqs 218s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa 218s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa 218s CMD finished (0 seconds) 218s CMD finished (0 seconds) 218s CMD: touch left.fa.ok 218s CMD finished (0 seconds) 218s CMD: touch right.fa.ok 218s CMD finished (0 seconds) 218s Done converting input files.CMD: cat left.fa right.fa > both.fa 218s CMD finished (0 seconds) 218s CMD: touch both.fa.ok 218s CMD finished (0 seconds) 218s -kmer counting. 218s ------------------------------------------- 218s ----------- Jellyfish -------------------- 218s -- (building a k-mer catalog from reads) -- 218s ------------------------------------------- 218s 218s CMD: jellyfish count -t 1 -m 25 -s 100000000 both.fa 221s CMD finished (3 seconds) 221s CMD: jellyfish histo -t 1 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 221s CMD finished (0 seconds) 221s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 221s CMD finished (0 seconds) 221s CMD: touch jellyfish.K25.min2.kmers.fa.success 221s CMD finished (0 seconds) 221s -generating stats files 221s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > left.fa.K25.stats 221s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > right.fa.K25.stats 221s -reading Kmer occurrences... 221s -reading Kmer occurrences... 221s 221s done parsing 100973 Kmers, 100873 added, taking 0 seconds. 221s 221s done parsing 100973 Kmers, 100873 added, taking 0 seconds. 222s STATS_GENERATION_TIME: 1 seconds. 222s CMD finished (1 seconds) 222s STATS_GENERATION_TIME: 1 seconds. 222s CMD finished (1 seconds) 222s CMD: touch left.fa.K25.stats.ok 222s CMD finished (0 seconds) 222s CMD: touch right.fa.K25.stats.ok 222s CMD finished (0 seconds) 222s -sorting each stats file by read name. 222s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=1 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort 222s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=1 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort 222s CMD finished (0 seconds) 222s CMD finished (0 seconds) 222s CMD: touch left.fa.K25.stats.sort.ok 222s CMD finished (0 seconds) 222s CMD: touch right.fa.K25.stats.sort.ok 222s CMD finished (0 seconds) 222s -defining normalized reads 222s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats 222s -opening left.fa.K25.stats.sort 222s -opening right.fa.K25.stats.sort 222s -done opening files. 223s CMD finished (1 seconds) 223s CMD: touch pairs.K25.stats.ok 223s CMD finished (0 seconds) 223s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200 --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs 224s 30472 / 30575 = 99.66% reads selected during normalization. 224s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles. 224s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1 224s CMD finished (1 seconds) 224s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 224s CMD finished (0 seconds) 224s -search and capture. 224s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture. 224s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz 224s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture. 224s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz 225s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 225s CMD finished (0 seconds) 225s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 225s CMD finished (0 seconds) 225s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq 225s CMD finished (0 seconds) 225s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq 225s CMD finished (0 seconds) 225s 225s 225s Normalization complete. See outputs: 225s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq 225s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq 225s Saturday, November 2, 2024: 17:40:41 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/normalization.ok 225s Converting input files. (in parallel)Saturday, November 2, 2024: 17:40:41 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa 225s Saturday, November 2, 2024: 17:40:41 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa 225s Saturday, November 2, 2024: 17:40:41 CMD: touch right.fa.ok 225s Saturday, November 2, 2024: 17:40:41 CMD: touch left.fa.ok 225s Saturday, November 2, 2024: 17:40:41 CMD: touch left.fa.ok right.fa.ok 225s Saturday, November 2, 2024: 17:40:41 CMD: cat left.fa right.fa > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa 225s Saturday, November 2, 2024: 17:40:41 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa.ok 225s ------------------------------------------- 225s ----------- Jellyfish -------------------- 225s -- (building a k-mer (25) catalog from reads) -- 225s ------------------------------------------- 225s 225s * [Sat Nov 2 17:40:41 2024] Running CMD: jellyfish count -t 1 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa 228s * [Sat Nov 2 17:40:45 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 229s * [Sat Nov 2 17:40:45 2024] Running CMD: jellyfish histo -t 1 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 229s ---------------------------------------------- 229s --------------- Inchworm (K=25, asm) --------------------- 229s -- (Linear contig construction from k-mers) -- 229s ---------------------------------------------- 229s 229s * [Sat Nov 2 17:40:45 2024] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --keep_tmp_files --num_threads 1 --PARALLEL_IWORM --min_any_entropy 1.0 -L 25 --no_prune_error_kmers > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa.tmp 229s Kmer length set to: 25 229s Min assembly length set to: 25 229s Monitor turned on, set to: 1 229s -retaining tmp files 229s min entropy set to: 1 229s setting number of threads to: 1 229s -setting parallel iworm mode. 229s -reading Kmer occurrences... 230s [0M] Kmers parsed. [0M] Kmers parsed. [0M] Kmers parsed. [0M] Kmers parsed. [0M] Kmers parsed. 230s done parsing 519541 Kmers, 519541 added, taking 1 seconds. 230s 230s TIMING KMER_DB_BUILDING 1 s. 230s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 230s Pruned 4252 kmers from catalog. 230s Pruning time: 0 seconds = 0 minutes. 230s 230s TIMING PRUNING 0 s. 230s -populating the kmer seed candidate list. 230s Kcounter hash size: 519541 230s Processed 515289 non-zero abundance kmers in kcounter. 230s -Not sorting list of kmers, given parallel mode in effect. 230s -beginning inchworm contig assembly. 230s Total kcounter hash size: 519541 vs. sorted list size: 515289 230s num threads set to: 1 230s Done opening file. tmp.iworm.fa.pid_8534.thread_0 231s 231s Iworm contig assembly time: 1 seconds = 0.0166667 minutes. 231s 231s TIMING CONTIG_BUILDING 1 s. 231s 231s TIMING PROG_RUNTIME 2 s. 231s * [Sat Nov 2 17:40:47 2024] Running CMD: mv /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa.tmp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa 231s Saturday, November 2, 2024: 17:40:47 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa.finished 231s -------------------------------------------------------- 231s -------------------- Chrysalis ------------------------- 231s -- (Contig Clustering & de Bruijn Graph Construction) -- 231s -------------------------------------------------------- 231s 231s inchworm_target: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa 231s bowtie_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa 231s chrysalis_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa 231s * [Sat Nov 2 17:40:47 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa 100 10 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 231s * [Sat Nov 2 17:40:47 2024] Running CMD: /usr/bin/bowtie2-build --threads 1 -o 3 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 1>/dev/null 231s * [Sat Nov 2 17:40:47 2024] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 1 -f --score-min G,20,8 -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa | samtools view -@ 1 -F4 -Sb - | samtools sort -m 1073741824 -@ 1 -no /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" 237s * [Sat Nov 2 17:40:53 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_scaffolds.txt 237s * [Sat Nov 2 17:40:53 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 1 -k 24 -kk 48 -strand -scaffolding /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt 239s * [Sat Nov 2 17:40:55 2024] Running CMD: /usr/bin/sort --parallel=1 -T . -S 2G -k9,9gr /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted 239s * [Sat Nov 2 17:40:55 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 239s * [Sat Nov 2 17:40:55 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 -weld_graph /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/GraphFromIwormFasta.out 239s * [Sat Nov 2 17:40:55 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200 239s * [Sat Nov 2 17:40:55 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa -f /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/readsToComponents.out -t 1 -max_mem_reads 50000000 -strand -p 10 243s * [Sat Nov 2 17:40:59 2024] Running CMD: /usr/bin/sort --parallel=1 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/readsToComponents.out > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/readsToComponents.out.sort 243s Saturday, November 2, 2024: 17:40:59 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/read_partitions/Fb_0/CBin_0 244s Saturday, November 2, 2024: 17:41:00 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/partitioned_reads.files.list.ok 244s Saturday, November 2, 2024: 17:41:00 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --SS_lib_type F --seqType fa --trinity_complete --no_cleanup --no_salmon > recursive_trinity.cmds 244s Saturday, November 2, 2024: 17:41:00 CMD: touch recursive_trinity.cmds.ok 244s Saturday, November 2, 2024: 17:41:00 CMD: touch recursive_trinity.cmds.ok 244s 244s 244s -------------------------------------------------------------------------------- 244s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 244s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 244s -------------------------------------------------------------------------------- 244s 244s Saturday, November 2, 2024: 17:41:00 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 1 -v -shuffle 244s Number of Commands: 36 360s succeeded(1) 2.77778% completed. succeeded(2) 5.55556% completed. succeeded(3) 8.33333% completed. succeeded(4) 11.1111% completed. succeeded(5) 13.8889% completed. succeeded(6) 16.6667% completed. succeeded(7) 19.4444% completed. succeeded(8) 22.2222% completed. succeeded(9) 25% completed. succeeded(10) 27.7778% completed. succeeded(11) 30.5556% completed. succeeded(12) 33.3333% completed. succeeded(13) 36.1111% completed. succeeded(14) 38.8889% completed. succeeded(15) 41.6667% completed. succeeded(16) 44.4444% completed. succeeded(17) 47.2222% completed. succeeded(18) 50% completed. succeeded(19) 52.7778% completed. succeeded(20) 55.5556% completed. succeeded(21) 58.3333% completed. succeeded(22) 61.1111% completed. succeeded(23) 63.8889% completed. succeeded(24) 66.6667% completed. succeeded(25) 69.4444% completed. succeeded(26) 72.2222% completed. succeeded(27) 75% completed. succeeded(28) 77.7778% completed. succeeded(29) 80.5556% completed. succeeded(30) 83.3333% completed. succeeded(31) 86.1111% completed. succeeded(32) 88.8889% completed. succeeded(33) 91.6667% completed. succeeded(34) 94.4444% completed. succeeded(35) 97.2222% completed. succeeded(36) 100% completed. 360s 360s All commands completed successfully. :-) 360s 360s 360s 360s ** Harvesting all assembled transcripts into a single multi-fasta file... 360s 360s Saturday, November 2, 2024: 17:42:56 CMD: find /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/read_partitions/ -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.tmp 360s * [Sat Nov 2 17:42:56 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa 1 362s * [Sat Nov 2 17:42:58 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta 362s Saturday, November 2, 2024: 17:42:58 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta.gene_trans_map 362s 362s 362s ############################################################################# 362s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta 362s ############################################################################# 362s 362s 362s 362s ##### Done Running Trinity ##### 362s 362s if [ $* ]; then 362s # check full-length reconstruction stats: 362s 362s ${TRINITY_HOME}/util/misc/illustrate_ref_comparison.pl __indiv_ex_sample_derived/refSeqs.fa trinity_out_dir.Trinity.fasta 90 362s 362s ./test_FL.sh --query trinity_out_dir.Trinity.fasta --target __indiv_ex_sample_derived/refSeqs.fa --no_reuse 362s 362s fi 362s 362s ./misc_run_tests/__test_runMe_NO_normalization.sh 362s #!/bin/bash -ve 362s 362s 362s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then 362s gunzip -c reads.right.fq.gz > reads.right.fq 362s fi 362s 362s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then 362s gunzip -c reads.left.fq.gz > reads.left.fq 362s fi 362s 362s 362s 362s ####################################################### 362s ## Run Trinity to Generate Transcriptome Assemblies ## 362s ####################################################### 362s 362s CPU=$(nproc || sysctl -n hw.physicalcpu) 362s 362s ## use jellyfish 362s ${TRINITY_HOME}/Trinity --seqType fq \ 362s --max_memory 2G \ 362s --left reads.left.fq \ 362s --right reads.right.fq \ 362s --SS_lib_type RF \ 362s --CPU ${CPU} \ 362s --no_normalize_reads \ 362s --output __test_trinity_wo_normalization 362s 362s 362s ______ ____ ____ ____ ____ ______ __ __ 362s | || \ | || \ | || || | | 362s | || D ) | | | _ | | | | || | | 362s |_| |_|| / | | | | | | | |_| |_|| ~ | 362s | | | \ | | | | | | | | | |___, | 362s | | | . \ | | | | | | | | | | | 362s |__| |__|\_||____||__|__||____| |__| |____/ 362s 362s Trinity-v2.15.1 362s 362s 362s 362s Left read files: $VAR1 = [ 362s 'reads.left.fq' 362s ]; 362s Right read files: $VAR1 = [ 362s 'reads.right.fq' 362s ]; 363s Saturday, November 2, 2024: 17:42:59 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization 363s Saturday, November 2, 2024: 17:42:59 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis 363s 363s 363s ---------------------------------------------------------------------------------- 363s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 363s ---------------------------------------------------------------------------------- 363s 363s Converting input files. (in parallel)Saturday, November 2, 2024: 17:42:59 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa 363s Saturday, November 2, 2024: 17:42:59 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq | seqtk-trinity seq -A -R 2 - >> right.fa 363s Saturday, November 2, 2024: 17:42:59 CMD: touch right.fa.ok 363s Saturday, November 2, 2024: 17:42:59 CMD: touch left.fa.ok 363s Saturday, November 2, 2024: 17:42:59 CMD: touch left.fa.ok right.fa.ok 363s Saturday, November 2, 2024: 17:42:59 CMD: cat left.fa right.fa > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa 363s Saturday, November 2, 2024: 17:42:59 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa.ok 363s ------------------------------------------- 363s ----------- Jellyfish -------------------- 363s -- (building a k-mer (25) catalog from reads) -- 363s ------------------------------------------- 363s 363s * [Sat Nov 2 17:42:59 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa 364s * [Sat Nov 2 17:43:00 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 365s * [Sat Nov 2 17:43:01 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 365s ---------------------------------------------- 365s --------------- Inchworm (K=25, asm) --------------------- 365s -- (Linear contig construction from k-mers) -- 365s ---------------------------------------------- 365s 365s * [Sat Nov 2 17:43:01 2024] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --num_threads 2 --PARALLEL_IWORM --min_any_entropy 1.0 -L 25 --no_prune_error_kmers > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa.tmp 365s Kmer length set to: 25 365s Min assembly length set to: 25 365s Monitor turned on, set to: 1 365s min entropy set to: 1 365s setting number of threads to: 2 365s -setting parallel iworm mode. 365s -reading Kmer occurrences... 365s [0M] Kmers parsed. [0M] Kmers parsed. 365s done parsing 520108 Kmers, 520108 added, taking 0 seconds. 365s 365s TIMING KMER_DB_BUILDING 0 s. 365s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 366s Pruned 4291 kmers from catalog. 366s Pruning time: 1 seconds = 0.0166667 minutes. 366s 366s TIMING PRUNING 1 s. 366s -populating the kmer seed candidate list. 366s Kcounter hash size: 520108 366s Processed 515817 non-zero abundance kmers in kcounter. 366s -Not sorting list of kmers, given parallel mode in effect. 366s -beginning inchworm contig assembly. 366s Total kcounter hash size: 520108 vs. sorted list size: 515817 366s num threads set to: 2 366s Done opening file. tmp.iworm.fa.pid_14811.thread_0 366s Done opening file. tmp.iworm.fa.pid_14811.thread_1 366s 366s Iworm contig assembly time: 0 seconds = 0 minutes. 366s 366s TIMING CONTIG_BUILDING 0 s. 366s 366s TIMING PROG_RUNTIME 1 s. 366s * [Sat Nov 2 17:43:02 2024] Running CMD: mv /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa.tmp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa 366s Saturday, November 2, 2024: 17:43:02 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa.finished 366s -------------------------------------------------------- 366s -------------------- Chrysalis ------------------------- 366s -- (Contig Clustering & de Bruijn Graph Construction) -- 366s -------------------------------------------------------- 366s 366s inchworm_target: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa 366s bowtie_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa 366s chrysalis_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa 366s * [Sat Nov 2 17:43:03 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa 100 10 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 367s * [Sat Nov 2 17:43:03 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 1>/dev/null 367s * [Sat Nov 2 17:43:03 2024] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa | samtools view -@ 2 -F4 -Sb - | samtools sort -m 536870912 -@ 2 -no /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm.bowtie.nameSorted.bam" 372s * [Sat Nov 2 17:43:08 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_scaffolds.txt 373s * [Sat Nov 2 17:43:09 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48 -strand -scaffolding /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt 378s * [Sat Nov 2 17:43:14 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k9,9gr /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted 378s * [Sat Nov 2 17:43:14 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 378s * [Sat Nov 2 17:43:14 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 -weld_graph /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/GraphFromIwormFasta.out 378s * [Sat Nov 2 17:43:14 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/bundled_iworm_contigs.fasta -min 200 378s * [Sat Nov 2 17:43:14 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa -f /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -strand -p 10 381s * [Sat Nov 2 17:43:17 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/readsToComponents.out > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/readsToComponents.out.sort 381s Saturday, November 2, 2024: 17:43:17 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/read_partitions/Fb_0/CBin_0 381s Saturday, November 2, 2024: 17:43:17 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/partitioned_reads.files.list.ok 381s Saturday, November 2, 2024: 17:43:17 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --SS_lib_type F --seqType fa --trinity_complete --full_cleanup --no_salmon > recursive_trinity.cmds 381s Saturday, November 2, 2024: 17:43:17 CMD: touch recursive_trinity.cmds.ok 381s Saturday, November 2, 2024: 17:43:17 CMD: touch recursive_trinity.cmds.ok 381s 381s 381s -------------------------------------------------------------------------------- 381s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 381s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 381s -------------------------------------------------------------------------------- 381s 381s Saturday, November 2, 2024: 17:43:17 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 381s Number of Commands: 41 466s succeeded(1) 2.43902% completed. succeeded(2) 4.87805% completed. succeeded(3) 7.31707% completed. succeeded(4) 9.7561% completed. succeeded(5) 12.1951% completed. succeeded(6) 14.6341% completed. succeeded(7) 17.0732% completed. succeeded(8) 19.5122% completed. succeeded(9) 21.9512% completed. succeeded(10) 24.3902% completed. succeeded(11) 26.8293% completed. succeeded(12) 29.2683% completed. succeeded(13) 31.7073% completed. succeeded(14) 34.1463% completed. succeeded(15) 36.5854% completed. succeeded(16) 39.0244% completed. succeeded(17) 41.4634% completed. succeeded(18) 43.9024% completed. succeeded(19) 46.3415% completed. succeeded(20) 48.7805% completed. succeeded(21) 51.2195% completed. succeeded(22) 53.6585% completed. succeeded(23) 56.0976% completed. succeeded(24) 58.5366% completed. succeeded(25) 60.9756% completed. succeeded(26) 63.4146% completed. succeeded(27) 65.8537% completed. succeeded(28) 68.2927% completed. succeeded(29) 70.7317% completed. succeeded(30) 73.1707% completed. succeeded(31) 75.6098% completed. succeeded(32) 78.0488% completed. succeeded(33) 80.4878% completed. succeeded(34) 82.9268% completed. succeeded(35) 85.3659% completed. succeeded(36) 87.8049% completed. succeeded(37) 90.2439% completed. succeeded(38) 92.6829% completed. succeeded(39) 95.1219% completed. succeeded(40) 97.561% completed. succeeded(41) 100% completed. 466s 466s All commands completed successfully. :-) 466s 466s 466s 466s ** Harvesting all assembled transcripts into a single multi-fasta file... 466s 466s Saturday, November 2, 2024: 17:44:42 CMD: find /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/read_partitions/ -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/Trinity.tmp 466s * [Sat Nov 2 17:44:42 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa 2 468s * [Sat Nov 2 17:44:44 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta 468s Saturday, November 2, 2024: 17:44:44 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta.gene_trans_map 468s 468s 468s ############################################################################# 468s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta 468s ############################################################################# 468s 468s 468s 468s 468s 468s ./misc_run_tests/__runMe_with_qual_trimming.sh 468s #!/bin/bash -ve 468s 468s 468s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then 468s gunzip -c reads.right.fq.gz > reads.right.fq 468s fi 468s 468s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then 468s gunzip -c reads.left.fq.gz > reads.left.fq 468s fi 468s 468s 468s 468s ####################################################### 468s ## Run Trinity to Generate Transcriptome Assemblies ## 468s ####################################################### 468s 468s CPU=$(nproc || sysctl -n hw.physicalcpu) 468s 468s ${TRINITY_HOME}/Trinity \ 468s --seqType fq \ 468s --max_memory 2G \ 468s --left reads.left.fq \ 468s --right reads.right.fq \ 468s --SS_lib_type RF \ 468s --CPU ${CPU} \ 468s --no_normalize_reads \ 468s --trimmomatic \ 468s --output __test_trinity_with_trimmomatic 468s 468s 468s ______ ____ ____ ____ ____ ______ __ __ 468s | || \ | || \ | || || | | 468s | || D ) | | | _ | | | | || | | 468s |_| |_|| / | | | | | | | |_| |_|| ~ | 468s | | | \ | | | | | | | | | |___, | 468s | | | . \ | | | | | | | | | | | 468s |__| |__|\_||____||__|__||____| |__| |____/ 468s 468s Trinity-v2.15.1 468s 468s 468s 468s Left read files: $VAR1 = [ 468s 'reads.left.fq' 468s ]; 468s Right read files: $VAR1 = [ 468s 'reads.right.fq' 468s ]; 468s Saturday, November 2, 2024: 17:44:44 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic 468s Saturday, November 2, 2024: 17:44:44 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis 468s 468s 468s ---------------------------------------------------------------------------------- 468s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 468s ---------------------------------------------------------------------------------- 468s 468s --------------------------------------------------------------- 468s ------ Quality Trimming Via Trimmomatic --------------------- 468s << ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >> 468s --------------------------------------------------------------- 468s 468s 468s ## Running Trimmomatic on read files: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq, /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq 468s Saturday, November 2, 2024: 17:44:44 CMD: java -jar /usr/share/java/trimmomatic.jar PE -threads 2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 468s TrimmomaticPE: Started with arguments: 468s -threads 2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 468s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' 468s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences 468s Quality encoding detected as phred33 469s Input Read Pairs: 30575 Both Surviving: 27726 (90.68%) Forward Only Surviving: 746 (2.44%) Reverse Only Surviving: 722 (2.36%) Dropped: 1381 (4.52%) 469s TrimmomaticPE: Completed successfully 469s Saturday, November 2, 2024: 17:44:45 CMD: cat reads.left.fq.P.qtrim reads.left.fq.U.qtrim > reads.left.fq.PwU.qtrim.fq 469s Saturday, November 2, 2024: 17:44:45 CMD: cat reads.right.fq.P.qtrim reads.right.fq.U.qtrim > reads.right.fq.PwU.qtrim.fq 469s Saturday, November 2, 2024: 17:44:45 CMD: touch trimmomatic.ok 469s Saturday, November 2, 2024: 17:44:45 CMD: gzip reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim & 469s Converting input files. (in parallel)Saturday, November 2, 2024: 17:44:45 CMD: cat reads.left.fq.PwU.qtrim.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa 469s Saturday, November 2, 2024: 17:44:45 CMD: cat reads.right.fq.PwU.qtrim.fq | seqtk-trinity seq -A -R 2 - >> right.fa 469s Saturday, November 2, 2024: 17:44:45 CMD: touch right.fa.ok 469s Saturday, November 2, 2024: 17:44:45 CMD: touch left.fa.ok 469s Saturday, November 2, 2024: 17:44:45 CMD: touch left.fa.ok right.fa.ok 469s Saturday, November 2, 2024: 17:44:45 CMD: cat left.fa right.fa > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa 469s Saturday, November 2, 2024: 17:44:45 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa.ok 469s ------------------------------------------- 469s ----------- Jellyfish -------------------- 469s -- (building a k-mer (25) catalog from reads) -- 469s ------------------------------------------- 469s 469s * [Sat Nov 2 17:44:45 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa 471s * [Sat Nov 2 17:44:47 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 471s * [Sat Nov 2 17:44:47 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 471s ---------------------------------------------- 471s --------------- Inchworm (K=25, asm) --------------------- 471s -- (Linear contig construction from k-mers) -- 471s ---------------------------------------------- 471s 471s * [Sat Nov 2 17:44:47 2024] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --num_threads 2 --PARALLEL_IWORM --min_any_entropy 1.0 -L 25 --no_prune_error_kmers > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa.tmp 471s Kmer length set to: 25 471s Min assembly length set to: 25 471s Monitor turned on, set to: 1 471s min entropy set to: 1 471s setting number of threads to: 2 471s -setting parallel iworm mode. 471s -reading Kmer occurrences... 472s [0M] Kmers parsed. 472s done parsing 318541 Kmers, 318541 added, taking 1 seconds. 472s 472s TIMING KMER_DB_BUILDING 1 s. 472s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 472s Pruned 1498 kmers from catalog. 472s Pruning time: 0 seconds = 0 minutes. 472s 472s TIMING PRUNING 0 s. 472s -populating the kmer seed candidate list. 472s Kcounter hash size: 318541 472s Processed 317043 non-zero abundance kmers in kcounter. 472s -Not sorting list of kmers, given parallel mode in effect. 472s -beginning inchworm contig assembly. 472s Total kcounter hash size: 318541 vs. sorted list size: 317043 472s num threads set to: 2 472s Done opening file. tmp.iworm.fa.pid_22049.thread_0 472s Done opening file. tmp.iworm.fa.pid_22049.thread_1 472s 472s Iworm contig assembly time: 0 seconds = 0 minutes. 472s 472s TIMING CONTIG_BUILDING 0 s. 472s 472s TIMING PROG_RUNTIME 1 s. 472s * [Sat Nov 2 17:44:48 2024] Running CMD: mv /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa.tmp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa 472s Saturday, November 2, 2024: 17:44:48 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa.finished 472s -------------------------------------------------------- 472s -------------------- Chrysalis ------------------------- 472s -- (Contig Clustering & de Bruijn Graph Construction) -- 472s -------------------------------------------------------- 472s 472s inchworm_target: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa 472s bowtie_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa 472s chrysalis_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa 472s * [Sat Nov 2 17:44:48 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa 100 10 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 472s * [Sat Nov 2 17:44:48 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 1>/dev/null 473s * [Sat Nov 2 17:44:49 2024] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa | samtools view -@ 2 -F4 -Sb - | samtools sort -m 536870912 -@ 2 -no /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm.bowtie.nameSorted.bam" 476s * [Sat Nov 2 17:44:52 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_scaffolds.txt 477s * [Sat Nov 2 17:44:53 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48 -strand -scaffolding /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt 481s * [Sat Nov 2 17:44:57 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k9,9gr /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted 481s * [Sat Nov 2 17:44:57 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 481s * [Sat Nov 2 17:44:57 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 -weld_graph /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/GraphFromIwormFasta.out 481s * [Sat Nov 2 17:44:57 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/bundled_iworm_contigs.fasta -min 200 481s * [Sat Nov 2 17:44:57 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa -f /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -strand -p 10 483s * [Sat Nov 2 17:44:59 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/readsToComponents.out > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/readsToComponents.out.sort 483s Saturday, November 2, 2024: 17:44:59 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/read_partitions/Fb_0/CBin_0 483s Saturday, November 2, 2024: 17:44:59 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/partitioned_reads.files.list.ok 483s Saturday, November 2, 2024: 17:44:59 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --SS_lib_type F --seqType fa --trinity_complete --full_cleanup --no_salmon > recursive_trinity.cmds 483s Saturday, November 2, 2024: 17:44:59 CMD: touch recursive_trinity.cmds.ok 483s Saturday, November 2, 2024: 17:44:59 CMD: touch recursive_trinity.cmds.ok 483s 483s 483s -------------------------------------------------------------------------------- 483s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 483s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 483s -------------------------------------------------------------------------------- 483s 483s Saturday, November 2, 2024: 17:44:59 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 483s Number of Commands: 35 556s succeeded(1) 2.85714% completed. succeeded(2) 5.71429% completed. succeeded(3) 8.57143% completed. succeeded(4) 11.4286% completed. succeeded(5) 14.2857% completed. succeeded(6) 17.1429% completed. succeeded(7) 20% completed. succeeded(8) 22.8571% completed. succeeded(9) 25.7143% completed. succeeded(10) 28.5714% completed. succeeded(11) 31.4286% completed. succeeded(12) 34.2857% completed. succeeded(13) 37.1429% completed. succeeded(14) 40% completed. succeeded(15) 42.8571% completed. succeeded(16) 45.7143% completed. succeeded(17) 48.5714% completed. succeeded(18) 51.4286% completed. succeeded(19) 54.2857% completed. succeeded(20) 57.1429% completed. succeeded(21) 60% completed. succeeded(22) 62.8571% completed. succeeded(23) 65.7143% completed. succeeded(24) 68.5714% completed. succeeded(25) 71.4286% completed. succeeded(26) 74.2857% completed. succeeded(27) 77.1429% completed. succeeded(28) 80% completed. succeeded(29) 82.8571% completed. succeeded(30) 85.7143% completed. succeeded(31) 88.5714% completed. succeeded(32) 91.4286% completed. succeeded(33) 94.2857% completed. succeeded(34) 97.1429% completed. succeeded(35) 100% completed. 556s 556s All commands completed successfully. :-) 556s 556s 556s 556s ** Harvesting all assembled transcripts into a single multi-fasta file... 556s 556s Saturday, November 2, 2024: 17:46:12 CMD: find /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/read_partitions/ -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/Trinity.tmp 556s * [Sat Nov 2 17:46:12 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa 2 557s * [Sat Nov 2 17:46:13 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta 557s Saturday, November 2, 2024: 17:46:13 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta.gene_trans_map 557s 557s 557s ############################################################################# 557s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta 557s ############################################################################# 557s 557s 557s 557s ##### Done Running Trinity ##### 557s 557s #!/bin/bash -ve 557s 557s 557s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then 557s gunzip -c reads.right.fq.gz > reads.right.fq 557s fi 557s 557s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then 557s gunzip -c reads.left.fq.gz > reads.left.fq 557s fi 557s 557s 557s 557s ####################################################### 557s ## Run Trinity to Generate Transcriptome Assemblies ## 557s ####################################################### 557s 557s CPU=$(nproc || sysctl -n hw.physicalcpu) 557s ./misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh 557s 557s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU ${CPU} --trimmomatic --normalize_reads --output __test_trinity_qual_and_norm 557s 557s 557s ______ ____ ____ ____ ____ ______ __ __ 557s | || \ | || \ | || || | | 557s | || D ) | | | _ | | | | || | | 557s |_| |_|| / | | | | | | | |_| |_|| ~ | 557s | | | \ | | | | | | | | | |___, | 557s | | | . \ | | | | | | | | | | | 557s |__| |__|\_||____||__|__||____| |__| |____/ 557s 557s Trinity-v2.15.1 557s 557s 557s 557s Left read files: $VAR1 = [ 557s 'reads.left.fq' 557s ]; 557s Right read files: $VAR1 = [ 557s 'reads.right.fq' 557s ]; 557s Saturday, November 2, 2024: 17:46:13 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm 557s Saturday, November 2, 2024: 17:46:13 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis 557s 557s 557s ---------------------------------------------------------------------------------- 557s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 557s ---------------------------------------------------------------------------------- 557s 557s --------------------------------------------------------------- 557s ------ Quality Trimming Via Trimmomatic --------------------- 557s << ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >> 557s --------------------------------------------------------------- 557s 557s 557s ## Running Trimmomatic on read files: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq, /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq 557s Saturday, November 2, 2024: 17:46:13 CMD: java -jar /usr/share/java/trimmomatic.jar PE -threads 2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 557s TrimmomaticPE: Started with arguments: 557s -threads 2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 557s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' 557s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences 558s Quality encoding detected as phred33 558s Input Read Pairs: 30575 Both Surviving: 27726 (90.68%) Forward Only Surviving: 746 (2.44%) Reverse Only Surviving: 722 (2.36%) Dropped: 1381 (4.52%) 558s TrimmomaticPE: Completed successfully 558s Saturday, November 2, 2024: 17:46:14 CMD: cp reads.left.fq.P.qtrim reads.left.fq.PwU.qtrim.fq 558s Saturday, November 2, 2024: 17:46:14 CMD: cp reads.right.fq.P.qtrim reads.right.fq.PwU.qtrim.fq 558s Saturday, November 2, 2024: 17:46:14 CMD: touch trimmomatic.ok 558s Saturday, November 2, 2024: 17:46:14 CMD: gzip reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim & 558s --------------------------------------------------------------- 558s ------------ In silico Read Normalization --------------------- 558s -- (Removing Excess Reads Beyond 200 Coverage -- 558s --------------------------------------------------------------- 558s 558s # running normalization on reads: $VAR1 = [ 558s [ 558s 'reads.left.fq.PwU.qtrim.fq' 558s ], 558s [ 558s 'reads.right.fq.PwU.qtrim.fq' 558s ] 558s ]; 558s 558s 558s Saturday, November 2, 2024: 17:46:14 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization --max_CV 10000 --SS_lib_type RF --left reads.left.fq.PwU.qtrim.fq --right reads.right.fq.PwU.qtrim.fq --pairs_together --PARALLEL_STATS 558s -prepping seqs 558s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.left.fq.PwU.qtrim.fq >> left.fa 558s CMD: seqtk-trinity seq -A -R 2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.right.fq.PwU.qtrim.fq >> right.fa 558s CMD finished (0 seconds) 558s CMD finished (0 seconds) 558s CMD: touch left.fa.ok 558s CMD finished (0 seconds) 558s CMD: touch right.fa.ok 558s CMD finished (0 seconds) 558s Done converting input files.CMD: cat left.fa right.fa > both.fa 558s CMD finished (0 seconds) 558s CMD: touch both.fa.ok 558s CMD finished (0 seconds) 558s -kmer counting. 558s ------------------------------------------- 558s ----------- Jellyfish -------------------- 558s -- (building a k-mer catalog from reads) -- 558s ------------------------------------------- 558s 558s CMD: jellyfish count -t 2 -m 25 -s 100000000 both.fa 560s CMD finished (2 seconds) 560s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 560s CMD finished (0 seconds) 560s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 560s CMD finished (0 seconds) 560s CMD: touch jellyfish.K25.min2.kmers.fa.success 560s CMD finished (0 seconds) 560s -generating stats files 560s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > left.fa.K25.stats 560s -reading Kmer occurrences... 560s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > right.fa.K25.stats 560s -reading Kmer occurrences... 561s 561s done parsing 88153 Kmers, 88076 added, taking 0 seconds. 561s 561s done parsing 88153 Kmers, 88076 added, taking 0 seconds. 561s STATS_GENERATION_TIME: 0 seconds. 561s CMD finished (0 seconds) 561s STATS_GENERATION_TIME: 0 seconds. 561s CMD finished (0 seconds) 561s CMD: touch left.fa.K25.stats.ok 561s CMD finished (0 seconds) 561s CMD: touch right.fa.K25.stats.ok 561s CMD finished (0 seconds) 561s -sorting each stats file by read name. 561s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort 561s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort 561s CMD finished (0 seconds) 561s CMD finished (0 seconds) 561s CMD: touch left.fa.K25.stats.sort.ok 561s CMD finished (0 seconds) 561s CMD: touch right.fa.K25.stats.sort.ok 561s CMD finished (0 seconds) 561s -defining normalized reads 561s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats 561s -opening left.fa.K25.stats.sort 561s -opening right.fa.K25.stats.sort 561s -done opening files. 562s CMD finished (1 seconds) 562s CMD: touch pairs.K25.stats.ok 562s CMD finished (0 seconds) 562s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200 --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs 562s 27678 / 27726 = 99.83% reads selected during normalization. 562s 0 / 27726 = 0.00% reads discarded as likely aberrant based on coverage profiles. 562s 0 / 27726 = 0.00% reads discarded as below minimum coverage threshold=1 562s CMD finished (0 seconds) 562s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 562s CMD finished (0 seconds) 562s -search and capture. 563s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.left.fq.PwU.qtrim.fq ... done prepping, now search and capture. 563s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.left.fq.PwU.qtrim.fq 563s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.right.fq.PwU.qtrim.fq ... done prepping, now search and capture. 563s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.right.fq.PwU.qtrim.fq 563s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/reads.left.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 563s CMD finished (0 seconds) 563s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/reads.right.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 563s CMD finished (0 seconds) 563s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/reads.left.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq 563s CMD finished (0 seconds) 563s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/reads.right.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq 563s CMD finished (0 seconds) 563s -removing tmp dir /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/tmp_normalized_reads 563s 563s 563s Normalization complete. See outputs: 563s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/reads.left.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq 563s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/reads.right.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq 563s Saturday, November 2, 2024: 17:46:19 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/normalization.ok 563s Converting input files. (in parallel)Saturday, November 2, 2024: 17:46:19 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa 563s Saturday, November 2, 2024: 17:46:19 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa 563s Saturday, November 2, 2024: 17:46:19 CMD: touch left.fa.ok 563s Saturday, November 2, 2024: 17:46:19 CMD: touch right.fa.ok 563s Saturday, November 2, 2024: 17:46:19 CMD: touch left.fa.ok right.fa.ok 563s Saturday, November 2, 2024: 17:46:19 CMD: cat left.fa right.fa > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa 563s Saturday, November 2, 2024: 17:46:19 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa.ok 563s ------------------------------------------- 563s ----------- Jellyfish -------------------- 563s -- (building a k-mer (25) catalog from reads) -- 563s ------------------------------------------- 563s 563s * [Sat Nov 2 17:46:19 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa 565s * [Sat Nov 2 17:46:21 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 565s * [Sat Nov 2 17:46:21 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 565s ---------------------------------------------- 565s --------------- Inchworm (K=25, asm) --------------------- 565s -- (Linear contig construction from k-mers) -- 565s ---------------------------------------------- 565s 565s * [Sat Nov 2 17:46:21 2024] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --num_threads 2 --PARALLEL_IWORM --min_any_entropy 1.0 -L 25 --no_prune_error_kmers > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa.tmp 565s Kmer length set to: 25 565s Min assembly length set to: 25 565s Monitor turned on, set to: 1 565s min entropy set to: 1 565s setting number of threads to: 2 565s -setting parallel iworm mode. 565s -reading Kmer occurrences... 565s [0M] Kmers parsed. 565s done parsing 311705 Kmers, 311705 added, taking 0 seconds. 565s 565s TIMING KMER_DB_BUILDING 0 s. 565s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 565s Pruned 1486 kmers from catalog. 565s Pruning time: 0 seconds = 0 minutes. 565s 565s TIMING PRUNING 0 s. 565s -populating the kmer seed candidate list. 565s Kcounter hash size: 311705 566s Processed 310219 non-zero abundance kmers in kcounter. 566s -Not sorting list of kmers, given parallel mode in effect. 566s -beginning inchworm contig assembly. 566s Total kcounter hash size: 311705 vs. sorted list size: 310219 566s num threads set to: 2 566s Done opening file. tmp.iworm.fa.pid_28346.thread_0 566s Done opening file. tmp.iworm.fa.pid_28346.thread_1 566s 566s Iworm contig assembly time: 0 seconds = 0 minutes. 566s 566s TIMING CONTIG_BUILDING 0 s. 566s 566s TIMING PROG_RUNTIME 1 s. 566s * [Sat Nov 2 17:46:22 2024] Running CMD: mv /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa.tmp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa 566s Saturday, November 2, 2024: 17:46:22 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa.finished 566s -------------------------------------------------------- 566s -------------------- Chrysalis ------------------------- 566s -- (Contig Clustering & de Bruijn Graph Construction) -- 566s -------------------------------------------------------- 566s 566s inchworm_target: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa 566s bowtie_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa 566s chrysalis_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa 566s * [Sat Nov 2 17:46:22 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa 100 10 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 566s * [Sat Nov 2 17:46:22 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 1>/dev/null 566s * [Sat Nov 2 17:46:22 2024] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa | samtools view -@ 2 -F4 -Sb - | samtools sort -m 536870912 -@ 2 -no /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm.bowtie.nameSorted.bam" 570s * [Sat Nov 2 17:46:26 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_scaffolds.txt 570s * [Sat Nov 2 17:46:26 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48 -strand -scaffolding /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt 573s * [Sat Nov 2 17:46:30 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k9,9gr /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted 573s * [Sat Nov 2 17:46:30 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 574s * [Sat Nov 2 17:46:30 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 -weld_graph /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/GraphFromIwormFasta.out 574s * [Sat Nov 2 17:46:30 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/bundled_iworm_contigs.fasta -min 200 574s * [Sat Nov 2 17:46:30 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa -f /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -strand -p 10 576s * [Sat Nov 2 17:46:32 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/readsToComponents.out > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/readsToComponents.out.sort 576s Saturday, November 2, 2024: 17:46:32 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/read_partitions/Fb_0/CBin_0 576s Saturday, November 2, 2024: 17:46:32 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/partitioned_reads.files.list.ok 576s Saturday, November 2, 2024: 17:46:32 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --SS_lib_type F --seqType fa --trinity_complete --full_cleanup --no_salmon > recursive_trinity.cmds 576s Saturday, November 2, 2024: 17:46:32 CMD: touch recursive_trinity.cmds.ok 576s Saturday, November 2, 2024: 17:46:32 CMD: touch recursive_trinity.cmds.ok 576s 576s 576s -------------------------------------------------------------------------------- 576s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 576s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 576s -------------------------------------------------------------------------------- 576s 576s Saturday, November 2, 2024: 17:46:32 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 576s Number of Commands: 39 648s succeeded(1) 2.5641% completed. succeeded(2) 5.12821% completed. succeeded(3) 7.69231% completed. succeeded(4) 10.2564% completed. succeeded(5) 12.8205% completed. succeeded(6) 15.3846% completed. succeeded(7) 17.9487% completed. succeeded(8) 20.5128% completed. succeeded(9) 23.0769% completed. succeeded(10) 25.641% completed. succeeded(11) 28.2051% completed. succeeded(12) 30.7692% completed. succeeded(13) 33.3333% completed. succeeded(14) 35.8974% completed. succeeded(15) 38.4615% completed. succeeded(16) 41.0256% completed. succeeded(17) 43.5897% completed. succeeded(18) 46.1538% completed. succeeded(19) 48.7179% completed. succeeded(20) 51.2821% completed. succeeded(21) 53.8462% completed. succeeded(22) 56.4103% completed. succeeded(23) 58.9744% completed. succeeded(24) 61.5385% completed. succeeded(25) 64.1026% completed. succeeded(26) 66.6667% completed. succeeded(27) 69.2308% completed. succeeded(28) 71.7949% completed. succeeded(29) 74.359% completed. succeeded(30) 76.9231% completed. succeeded(31) 79.4872% completed. succeeded(32) 82.0513% completed. succeeded(33) 84.6154% completed. succeeded(34) 87.1795% completed. succeeded(35) 89.7436% completed. succeeded(36) 92.3077% completed. succeeded(37) 94.8718% completed. succeeded(38) 97.4359% completed. succeeded(39) 100% completed. 648s 648s All commands completed successfully. :-) 648s 648s 648s 648s ** Harvesting all assembled transcripts into a single multi-fasta file... 648s 648s Saturday, November 2, 2024: 17:47:44 CMD: find /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/read_partitions/ -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/Trinity.tmp 648s * [Sat Nov 2 17:47:44 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa 2 649s * [Sat Nov 2 17:47:45 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta 649s Saturday, November 2, 2024: 17:47:45 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta.gene_trans_map 649s 649s 649s ############################################################################# 649s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta 649s ############################################################################# 649s 649s 649s 649s ##### Done Running Trinity ##### 649s 649s exit 0 649s #!/bin/bash -ve 649s 649s ${TRINITY_HOME}/Trinity --seqType fq --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU 1 --jaccard_clip --max_memory 1G --output __test_trinity_w_jaccard --grid_node_max_memory 2G --grid_node_CPU 2 649s ./misc_run_tests/__test_runMe_with_jaccard_clip.sh 649s 649s 649s ______ ____ ____ ____ ____ ______ __ __ 649s | || \ | || \ | || || | | 649s | || D ) | | | _ | | | | || | | 649s |_| |_|| / | | | | | | | |_| |_|| ~ | 649s | | | \ | | | | | | | | | |___, | 649s | | | . \ | | | | | | | | | | | 649s |__| |__|\_||____||__|__||____| |__| |____/ 649s 649s Trinity-v2.15.1 649s 649s 649s 649s Left read files: $VAR1 = [ 649s 'reads.left.fq.gz' 649s ]; 649s Right read files: $VAR1 = [ 649s 'reads.right.fq.gz' 649s ]; 649s Saturday, November 2, 2024: 17:47:45 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard 649s Saturday, November 2, 2024: 17:47:45 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis 649s 649s 649s ---------------------------------------------------------------------------------- 649s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 649s ---------------------------------------------------------------------------------- 649s 649s --------------------------------------------------------------- 649s ------------ In silico Read Normalization --------------------- 649s -- (Removing Excess Reads Beyond 200 Coverage -- 649s --------------------------------------------------------------- 649s 649s # running normalization on reads: $VAR1 = [ 649s [ 649s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz' 649s ], 649s [ 649s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz' 649s ] 649s ]; 649s 649s 649s Saturday, November 2, 2024: 17:47:45 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G --max_cov 200 --min_cov 1 --CPU 1 --output /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization --max_CV 10000 --SS_lib_type RF --left /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together --PARALLEL_STATS 649s -prepping seqs 649s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa 649s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa 649s CMD finished (0 seconds) 649s CMD finished (0 seconds) 649s CMD: touch left.fa.ok 649s CMD finished (0 seconds) 649s CMD: touch right.fa.ok 649s CMD finished (0 seconds) 649s Done converting input files.CMD: cat left.fa right.fa > both.fa 649s CMD finished (0 seconds) 649s CMD: touch both.fa.ok 649s CMD finished (0 seconds) 649s -kmer counting. 649s ------------------------------------------- 649s ----------- Jellyfish -------------------- 649s -- (building a k-mer catalog from reads) -- 649s ------------------------------------------- 649s 649s CMD: jellyfish count -t 1 -m 25 -s 100000000 both.fa 652s CMD finished (3 seconds) 652s CMD: jellyfish histo -t 1 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 652s CMD finished (0 seconds) 652s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 652s CMD finished (0 seconds) 652s CMD: touch jellyfish.K25.min2.kmers.fa.success 652s CMD finished (0 seconds) 652s -generating stats files 652s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > left.fa.K25.stats 652s -reading Kmer occurrences... 652s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > right.fa.K25.stats 652s -reading Kmer occurrences... 652s 652s done parsing 100973 Kmers, 100873 added, taking 0 seconds. 652s 652s done parsing 100973 Kmers, 100873 added, taking 0 seconds. 653s STATS_GENERATION_TIME: 1 seconds. 653s CMD finished (1 seconds) 653s STATS_GENERATION_TIME: 1 seconds. 653s CMD finished (1 seconds) 653s CMD: touch left.fa.K25.stats.ok 653s CMD finished (0 seconds) 653s CMD: touch right.fa.K25.stats.ok 653s CMD finished (0 seconds) 653s -sorting each stats file by read name. 653s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=1 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort 653s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=1 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort 653s CMD finished (0 seconds) 653s CMD finished (0 seconds) 653s CMD: touch left.fa.K25.stats.sort.ok 653s CMD finished (0 seconds) 653s CMD: touch right.fa.K25.stats.sort.ok 653s CMD finished (0 seconds) 653s -defining normalized reads 653s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats 653s -opening left.fa.K25.stats.sort 653s -opening right.fa.K25.stats.sort 653s -done opening files. 654s CMD finished (1 seconds) 654s CMD: touch pairs.K25.stats.ok 654s CMD finished (0 seconds) 654s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200 --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs 654s 30472 / 30575 = 99.66% reads selected during normalization. 654s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles. 654s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1 654s CMD finished (0 seconds) 654s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 654s CMD finished (0 seconds) 654s -search and capture. 654s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture. 654s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz 654s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture. 654s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz 655s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 655s CMD finished (0 seconds) 655s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 655s CMD finished (0 seconds) 655s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq 655s CMD finished (0 seconds) 655s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq 655s CMD finished (0 seconds) 655s -removing tmp dir /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/tmp_normalized_reads 655s 655s 655s Normalization complete. See outputs: 655s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq 655s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq 655s Saturday, November 2, 2024: 17:47:51 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/normalization.ok 655s Converting input files. (in parallel)Saturday, November 2, 2024: 17:47:51 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa 655s Saturday, November 2, 2024: 17:47:51 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa 655s Saturday, November 2, 2024: 17:47:51 CMD: touch left.fa.ok 655s Saturday, November 2, 2024: 17:47:51 CMD: touch right.fa.ok 655s Saturday, November 2, 2024: 17:47:51 CMD: touch left.fa.ok right.fa.ok 655s Saturday, November 2, 2024: 17:47:51 CMD: cat left.fa right.fa > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa 655s Saturday, November 2, 2024: 17:47:51 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa.ok 655s ------------------------------------------- 655s ----------- Jellyfish -------------------- 655s -- (building a k-mer (25) catalog from reads) -- 655s ------------------------------------------- 655s 655s * [Sat Nov 2 17:47:51 2024] Running CMD: jellyfish count -t 1 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa 658s * [Sat Nov 2 17:47:54 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 658s * [Sat Nov 2 17:47:54 2024] Running CMD: jellyfish histo -t 1 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 658s ---------------------------------------------- 658s --------------- Inchworm (K=25, asm) --------------------- 658s -- (Linear contig construction from k-mers) -- 658s ---------------------------------------------- 658s 658s * [Sat Nov 2 17:47:54 2024] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --num_threads 1 --PARALLEL_IWORM --min_any_entropy 1.0 -L 25 --no_prune_error_kmers > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa.tmp 658s Kmer length set to: 25 658s Min assembly length set to: 25 658s Monitor turned on, set to: 1 658s min entropy set to: 1 658s setting number of threads to: 1 658s -setting parallel iworm mode. 658s -reading Kmer occurrences... 659s [0M] Kmers parsed. [0M] Kmers parsed. [0M] Kmers parsed. [0M] Kmers parsed. [0M] Kmers parsed. 659s done parsing 519541 Kmers, 519541 added, taking 1 seconds. 659s 659s TIMING KMER_DB_BUILDING 1 s. 659s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 659s Pruned 4252 kmers from catalog. 659s Pruning time: 0 seconds = 0 minutes. 659s 659s TIMING PRUNING 0 s. 659s -populating the kmer seed candidate list. 659s Kcounter hash size: 519541 659s Processed 515289 non-zero abundance kmers in kcounter. 659s -Not sorting list of kmers, given parallel mode in effect. 659s -beginning inchworm contig assembly. 659s Total kcounter hash size: 519541 vs. sorted list size: 515289 659s num threads set to: 1 659s Done opening file. tmp.iworm.fa.pid_35277.thread_0 660s 660s Iworm contig assembly time: 1 seconds = 0.0166667 minutes. 660s 660s TIMING CONTIG_BUILDING 1 s. 660s 660s TIMING PROG_RUNTIME 2 s. 660s * [Sat Nov 2 17:47:56 2024] Running CMD: mv /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa.tmp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa 660s Saturday, November 2, 2024: 17:47:56 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa.finished 660s -------------------------------------------------------- 660s -------------------- Chrysalis ------------------------- 660s -- (Contig Clustering & de Bruijn Graph Construction) -- 660s -------------------------------------------------------- 660s 660s inchworm_target: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa 660s bowtie_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa 660s chrysalis_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa 660s * [Sat Nov 2 17:47:56 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa 100 10 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 660s * [Sat Nov 2 17:47:56 2024] Running CMD: /usr/bin/bowtie2-build --threads 1 -o 3 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 1>/dev/null 661s * [Sat Nov 2 17:47:57 2024] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 1 -f --score-min G,20,8 -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa | samtools view -@ 1 -F4 -Sb - | samtools sort -m 536870912 -@ 1 -no /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm.bowtie.nameSorted.bam" 666s * [Sat Nov 2 17:48:02 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_scaffolds.txt 666s * [Sat Nov 2 17:48:02 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 1 -k 24 -kk 48 -strand -scaffolding /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt 667s * [Sat Nov 2 17:48:03 2024] Running CMD: /usr/bin/sort --parallel=1 -T . -S 1G -k9,9gr /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted 667s * [Sat Nov 2 17:48:03 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 667s * [Sat Nov 2 17:48:04 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 -weld_graph /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/GraphFromIwormFasta.out 668s * [Sat Nov 2 17:48:04 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/bundled_iworm_contigs.fasta -min 200 668s * [Sat Nov 2 17:48:04 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa -f /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/readsToComponents.out -t 1 -max_mem_reads 50000000 -strand -p 10 672s * [Sat Nov 2 17:48:08 2024] Running CMD: /usr/bin/sort --parallel=1 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/readsToComponents.out > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/readsToComponents.out.sort 672s Saturday, November 2, 2024: 17:48:08 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0 672s Saturday, November 2, 2024: 17:48:08 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/partitioned_reads.files.list.ok 672s Saturday, November 2, 2024: 17:48:08 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/partitioned_reads.files.list --CPU 2 --max_memory 2G --run_as_paired --SS_lib_type F --seqType fa --trinity_complete --full_cleanup --jaccard_clip --no_salmon > recursive_trinity.cmds 672s Saturday, November 2, 2024: 17:48:08 CMD: touch recursive_trinity.cmds.ok 672s Saturday, November 2, 2024: 17:48:08 CMD: touch recursive_trinity.cmds.ok 672s 672s 672s -------------------------------------------------------------------------------- 672s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 672s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 672s -------------------------------------------------------------------------------- 672s 672s Saturday, November 2, 2024: 17:48:08 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 1 -v -shuffle 672s Number of Commands: 36 673s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 673s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 673s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 673s bt2 index files: $VAR1 = []; 673s Note - bowtie-build indices do not yet exist. Indexing genome now. 673s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 674s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 674s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 674s 9900 reads; of these: 674s 9900 (100.00%) were unpaired; of these: 674s 5 (0.05%) aligned 0 times 674s 5821 (58.80%) aligned exactly 1 time 674s 4074 (41.15%) aligned >1 times 674s 99.95% overall alignment rate 674s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 674s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 675s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 675s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 675s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam 675s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam 675s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 675s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam 675s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 675s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 675s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 675s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 675s 676s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 676s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 676s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 676s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 676s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 676s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 676s -processing jaccard pair sensor 677s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 677s [1000 lines read] scaff:a1;65 lend:476 rend:837 [2000 lines read] scaff:a1;65 lend:2420 rend:2904 [3000 lines read] scaff:a1;65 lend:3839 rend:4069 [4000 lines read] scaff:a1;65 lend:5020 rend:5460 [5000 lines read] scaff:a1;65 lend:5930 rend:6005 [6000 lines read] scaff:a22;4 lend:1 rend:49 [7000 lines read] scaff:a52;2 lend:1 rend:36 [8000 lines read] scaff:a65;2 lend:1 rend:36 [9000 lines read] scaff:a78;2 lend:2 rend:49 [10000 lines read] scaff:a90;2 lend:1 rend:37 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 677s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c4.trinity.reads.fa.out/inchworm.fa.clipped.fa 684s succeeded(1) 2.77778% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 684s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 684s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 684s bt2 index files: $VAR1 = []; 684s Note - bowtie-build indices do not yet exist. Indexing genome now. 684s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 684s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 684s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 684s 6 reads; of these: 684s 6 (100.00%) were unpaired; of these: 684s 0 (0.00%) aligned 0 times 684s 6 (100.00%) aligned exactly 1 time 684s 0 (0.00%) aligned >1 times 684s 100.00% overall alignment rate 684s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 684s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 684s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 684s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 684s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 684s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 684s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 684s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 684s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 684s 684s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 684s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 684s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 684s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 684s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 684s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 684s -processing jaccard pair sensor 684s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 684s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 684s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c28.trinity.reads.fa.out/inchworm.fa.clipped.fa 686s succeeded(2) 5.55556% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 686s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 686s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 686s bt2 index files: $VAR1 = []; 686s Note - bowtie-build indices do not yet exist. Indexing genome now. 686s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 686s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 686s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 686s 29 reads; of these: 686s 29 (100.00%) were unpaired; of these: 686s 0 (0.00%) aligned 0 times 686s 29 (100.00%) aligned exactly 1 time 686s 0 (0.00%) aligned >1 times 686s 100.00% overall alignment rate 687s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 687s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 687s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 687s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 687s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 687s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 687s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 687s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 687s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 687s 687s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 687s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 687s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 687s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 687s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 687s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 687s -processing jaccard pair sensor 687s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 687s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 687s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c11.trinity.reads.fa.out/inchworm.fa.clipped.fa 689s succeeded(3) 8.33333% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 689s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 689s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 689s bt2 index files: $VAR1 = []; 689s Note - bowtie-build indices do not yet exist. Indexing genome now. 689s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 689s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 689s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 689s 33 reads; of these: 689s 33 (100.00%) were unpaired; of these: 689s 0 (0.00%) aligned 0 times 689s 33 (100.00%) aligned exactly 1 time 689s 0 (0.00%) aligned >1 times 689s 100.00% overall alignment rate 689s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 689s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 689s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 689s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 689s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 689s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 689s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 689s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 689s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 689s 689s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 689s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 689s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 689s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 689s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 689s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 689s -processing jaccard pair sensor 689s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 689s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 689s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c15.trinity.reads.fa.out/inchworm.fa.clipped.fa 691s succeeded(4) 11.1111% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 691s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 691s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 691s bt2 index files: $VAR1 = []; 691s Note - bowtie-build indices do not yet exist. Indexing genome now. 691s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 692s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 692s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 692s 9 reads; of these: 692s 9 (100.00%) were unpaired; of these: 692s 0 (0.00%) aligned 0 times 692s 9 (100.00%) aligned exactly 1 time 692s 0 (0.00%) aligned >1 times 692s 100.00% overall alignment rate 692s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 692s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 692s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 692s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 692s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 692s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 692s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 692s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 692s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 692s 692s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 692s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 692s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 692s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 692s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 692s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 692s -processing jaccard pair sensor 692s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 692s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 692s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c24.trinity.reads.fa.out/inchworm.fa.clipped.fa 694s succeeded(5) 13.8889% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 694s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 694s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 694s bt2 index files: $VAR1 = []; 694s Note - bowtie-build indices do not yet exist. Indexing genome now. 694s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 694s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 694s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 694s 8 reads; of these: 694s 8 (100.00%) were unpaired; of these: 694s 0 (0.00%) aligned 0 times 694s 8 (100.00%) aligned exactly 1 time 694s 0 (0.00%) aligned >1 times 694s 100.00% overall alignment rate 694s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 694s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 694s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 694s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 694s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 694s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 694s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 694s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 694s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 694s 694s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 694s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 694s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 694s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 694s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 694s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 694s -processing jaccard pair sensor 694s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 694s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 694s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c35.trinity.reads.fa.out/inchworm.fa.clipped.fa 697s succeeded(6) 16.6667% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 697s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 697s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 697s bt2 index files: $VAR1 = []; 697s Note - bowtie-build indices do not yet exist. Indexing genome now. 697s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 697s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 697s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 698s 4987 reads; of these: 698s 4987 (100.00%) were unpaired; of these: 698s 2 (0.04%) aligned 0 times 698s 2643 (53.00%) aligned exactly 1 time 698s 2342 (46.96%) aligned >1 times 698s 99.96% overall alignment rate 698s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 698s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 698s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 698s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 698s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 698s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 698s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 698s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 698s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 698s 699s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 699s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 699s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 699s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 699s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 699s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 699s -processing jaccard pair sensor 699s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 699s [1000 lines read] scaff:a1;96 lend:803 rend:1291 [2000 lines read] scaff:a1;96 lend:1599 rend:1674 [3000 lines read] scaff:a24;3 lend:1 rend:34 [4000 lines read] scaff:a39;2 lend:1 rend:49 [5000 lines read] scaff:a49;2 lend:1 rend:53 [6000 lines read] scaff:a58;2 lend:3 rend:49 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 700s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c17.trinity.reads.fa.out/inchworm.fa.clipped.fa 704s succeeded(7) 19.4444% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 704s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 704s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 705s bt2 index files: $VAR1 = []; 705s Note - bowtie-build indices do not yet exist. Indexing genome now. 705s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 705s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 705s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 705s 15 reads; of these: 705s 15 (100.00%) were unpaired; of these: 705s 0 (0.00%) aligned 0 times 705s 15 (100.00%) aligned exactly 1 time 705s 0 (0.00%) aligned >1 times 705s 100.00% overall alignment rate 705s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 705s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 705s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 705s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 705s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 705s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 705s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 705s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 705s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 705s 705s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 705s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 705s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 705s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 705s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 705s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 705s -processing jaccard pair sensor 705s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 705s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 705s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c29.trinity.reads.fa.out/inchworm.fa.clipped.fa 707s succeeded(8) 22.2222% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 707s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 707s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 707s bt2 index files: $VAR1 = []; 707s Note - bowtie-build indices do not yet exist. Indexing genome now. 707s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 708s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 708s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 708s 17 reads; of these: 708s 17 (100.00%) were unpaired; of these: 708s 0 (0.00%) aligned 0 times 708s 17 (100.00%) aligned exactly 1 time 708s 0 (0.00%) aligned >1 times 708s 100.00% overall alignment rate 708s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 708s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 708s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 708s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 708s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 708s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 708s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 708s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 708s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 708s 708s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 708s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 708s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 708s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 708s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 708s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 708s -processing jaccard pair sensor 708s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 708s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 708s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c26.trinity.reads.fa.out/inchworm.fa.clipped.fa 711s succeeded(9) 25% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 711s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 711s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 711s bt2 index files: $VAR1 = []; 711s Note - bowtie-build indices do not yet exist. Indexing genome now. 711s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 711s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 711s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 711s 7052 reads; of these: 711s 7052 (100.00%) were unpaired; of these: 711s 4 (0.06%) aligned 0 times 711s 5120 (72.60%) aligned exactly 1 time 711s 1928 (27.34%) aligned >1 times 711s 99.94% overall alignment rate 711s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 711s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 712s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 712s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 712s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam 712s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam 712s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 712s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam 712s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 712s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 712s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 712s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 712s 712s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 712s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 712s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 712s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 712s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 712s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 712s -processing jaccard pair sensor 713s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 713s [1000 lines read] scaff:a1;37 lend:3075 rend:3272 [2000 lines read] scaff:a1;37 lend:5784 rend:6268 [3000 lines read] scaff:a1;37 lend:7480 rend:7705 [4000 lines read] scaff:a24;2 lend:1 rend:48 [5000 lines read] scaff:a55;2 lend:1 rend:44 [6000 lines read] scaff:a83;2 lend:1 rend:48 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 713s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c31.trinity.reads.fa.out/inchworm.fa.clipped.fa 725s succeeded(10) 27.7778% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 725s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 725s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 725s bt2 index files: $VAR1 = []; 725s Note - bowtie-build indices do not yet exist. Indexing genome now. 725s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 726s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 726s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 726s 7 reads; of these: 726s 7 (100.00%) were unpaired; of these: 726s 3 (42.86%) aligned 0 times 726s 4 (57.14%) aligned exactly 1 time 726s 0 (0.00%) aligned >1 times 726s 57.14% overall alignment rate 726s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 726s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 726s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 726s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 726s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 726s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 726s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 726s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 726s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 726s 726s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 726s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 726s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 726s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 726s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 726s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 726s -processing jaccard pair sensor 726s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 726s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 726s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c33.trinity.reads.fa.out/inchworm.fa.clipped.fa 727s succeeded(11) 30.5556% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 727s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 727s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 727s bt2 index files: $VAR1 = []; 727s Note - bowtie-build indices do not yet exist. Indexing genome now. 727s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 728s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 728s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 728s 28 reads; of these: 728s 28 (100.00%) were unpaired; of these: 728s 0 (0.00%) aligned 0 times 728s 28 (100.00%) aligned exactly 1 time 728s 0 (0.00%) aligned >1 times 728s 100.00% overall alignment rate 728s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 728s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 728s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 728s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 728s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 728s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 728s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 728s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 728s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 728s 728s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 728s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 728s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 728s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 728s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 728s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 728s -processing jaccard pair sensor 728s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 728s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 728s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/inchworm.fa.clipped.fa 731s succeeded(12) 33.3333% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 731s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 731s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 731s bt2 index files: $VAR1 = []; 731s Note - bowtie-build indices do not yet exist. Indexing genome now. 731s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 731s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 731s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 731s 24 reads; of these: 731s 24 (100.00%) were unpaired; of these: 731s 0 (0.00%) aligned 0 times 731s 24 (100.00%) aligned exactly 1 time 731s 0 (0.00%) aligned >1 times 731s 100.00% overall alignment rate 731s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 731s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 731s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 731s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 731s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 731s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 731s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 731s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 731s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 731s 731s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 731s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 731s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 731s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 731s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 731s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 731s -processing jaccard pair sensor 731s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 731s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 731s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/inchworm.fa.clipped.fa 734s succeeded(13) 36.1111% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 734s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 734s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 734s bt2 index files: $VAR1 = []; 734s Note - bowtie-build indices do not yet exist. Indexing genome now. 734s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 734s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 734s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 735s 5130 reads; of these: 735s 5130 (100.00%) were unpaired; of these: 735s 6 (0.12%) aligned 0 times 735s 4306 (83.94%) aligned exactly 1 time 735s 818 (15.95%) aligned >1 times 735s 99.88% overall alignment rate 735s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 735s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 735s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 735s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 735s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam 735s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam 735s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 735s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam 735s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 735s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 735s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 735s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 735s 735s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 735s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 735s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 735s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 735s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 735s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 735s -processing jaccard pair sensor 736s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 736s [1000 lines read] scaff:a25;2 lend:1 rend:45 [2000 lines read] scaff:a3;25 lend:514 rend:589 [3000 lines read] scaff:a3;25 lend:4028 rend:4299 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 736s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/inchworm.fa.clipped.fa 743s succeeded(14) 38.8889% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 743s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 743s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 743s bt2 index files: $VAR1 = []; 743s Note - bowtie-build indices do not yet exist. Indexing genome now. 743s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 743s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 743s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 743s 3374 reads; of these: 743s 3374 (100.00%) were unpaired; of these: 743s 1 (0.03%) aligned 0 times 743s 2870 (85.06%) aligned exactly 1 time 743s 503 (14.91%) aligned >1 times 743s 99.97% overall alignment rate 743s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 743s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 744s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 744s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 744s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam 744s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam 744s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 744s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam 744s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 744s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 744s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 744s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 744s 744s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 744s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 744s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 744s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 744s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 744s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 744s -processing jaccard pair sensor 744s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 744s [1000 lines read] scaff:a1;29 lend:1682 rend:1757 [2000 lines read] scaff:a1;29 lend:4783 rend:5150 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 744s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c0.trinity.reads.fa.out/inchworm.fa.clipped.fa 748s succeeded(15) 41.6667% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 748s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 748s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 748s bt2 index files: $VAR1 = []; 748s Note - bowtie-build indices do not yet exist. Indexing genome now. 748s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 748s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 748s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 749s 6 reads; of these: 749s 6 (100.00%) were unpaired; of these: 749s 0 (0.00%) aligned 0 times 749s 6 (100.00%) aligned exactly 1 time 749s 0 (0.00%) aligned >1 times 749s 100.00% overall alignment rate 749s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 749s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 749s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 749s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 749s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 749s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 749s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 749s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 749s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 749s 749s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 749s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 749s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 749s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 749s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 749s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 749s -processing jaccard pair sensor 749s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 749s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 749s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c23.trinity.reads.fa.out/inchworm.fa.clipped.fa 751s succeeded(16) 44.4444% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 751s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 751s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 751s bt2 index files: $VAR1 = []; 751s Note - bowtie-build indices do not yet exist. Indexing genome now. 751s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 751s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 751s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 751s 8 reads; of these: 751s 8 (100.00%) were unpaired; of these: 751s 0 (0.00%) aligned 0 times 751s 8 (100.00%) aligned exactly 1 time 751s 0 (0.00%) aligned >1 times 751s 100.00% overall alignment rate 751s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 751s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 751s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 751s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 751s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 751s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 751s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 751s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 751s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 751s 751s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 751s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 751s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 751s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 751s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 751s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 751s -processing jaccard pair sensor 751s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 751s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 751s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c25.trinity.reads.fa.out/inchworm.fa.clipped.fa 753s succeeded(17) 47.2222% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 753s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 753s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 753s bt2 index files: $VAR1 = []; 753s Note - bowtie-build indices do not yet exist. Indexing genome now. 753s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 753s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 753s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 753s 14 reads; of these: 753s 14 (100.00%) were unpaired; of these: 753s 0 (0.00%) aligned 0 times 753s 14 (100.00%) aligned exactly 1 time 753s 0 (0.00%) aligned >1 times 753s 100.00% overall alignment rate 753s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 753s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 753s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 753s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 753s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 753s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 753s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 753s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 754s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 754s 754s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 754s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 754s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 754s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 754s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 754s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 754s -processing jaccard pair sensor 754s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 754s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 754s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c18.trinity.reads.fa.out/inchworm.fa.clipped.fa 756s succeeded(18) 50% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 756s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 756s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 756s bt2 index files: $VAR1 = []; 756s Note - bowtie-build indices do not yet exist. Indexing genome now. 756s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 756s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 756s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 756s 15 reads; of these: 756s 15 (100.00%) were unpaired; of these: 756s 0 (0.00%) aligned 0 times 756s 15 (100.00%) aligned exactly 1 time 756s 0 (0.00%) aligned >1 times 756s 100.00% overall alignment rate 756s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 756s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 756s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 756s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 756s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 756s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 756s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 756s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 756s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 756s 756s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 756s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 756s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 756s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 756s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 756s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 756s -processing jaccard pair sensor 756s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 756s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 756s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c32.trinity.reads.fa.out/inchworm.fa.clipped.fa 759s succeeded(19) 52.7778% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 759s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 759s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 759s bt2 index files: $VAR1 = []; 759s Note - bowtie-build indices do not yet exist. Indexing genome now. 759s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 759s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 759s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 759s 2351 reads; of these: 759s 2351 (100.00%) were unpaired; of these: 759s 1 (0.04%) aligned 0 times 759s 1736 (73.84%) aligned exactly 1 time 759s 614 (26.12%) aligned >1 times 759s 99.96% overall alignment rate 759s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 759s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 760s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 760s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 760s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 760s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 760s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 760s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 760s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 760s 760s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 760s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 760s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 760s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 760s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 760s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 760s -processing jaccard pair sensor 760s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 760s [1000 lines read] scaff:a1;39 lend:1891 rend:2041 [2000 lines read] scaff:a42;2 lend:1 rend:49 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 760s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c8.trinity.reads.fa.out/inchworm.fa.clipped.fa 765s succeeded(20) 55.5556% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 765s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 765s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 765s bt2 index files: $VAR1 = []; 765s Note - bowtie-build indices do not yet exist. Indexing genome now. 765s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 766s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 766s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 766s 1875 reads; of these: 766s 1875 (100.00%) were unpaired; of these: 766s 2 (0.11%) aligned 0 times 766s 1543 (82.29%) aligned exactly 1 time 766s 330 (17.60%) aligned >1 times 766s 99.89% overall alignment rate 766s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 766s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 766s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 766s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 766s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 766s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 766s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 766s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 766s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 766s 766s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 766s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 766s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 766s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 766s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 766s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 766s -processing jaccard pair sensor 766s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 766s [1000 lines read] scaff:a21;2 lend:1 rend:49 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 767s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c5.trinity.reads.fa.out/inchworm.fa.clipped.fa 770s succeeded(21) 58.3333% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 770s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 770s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 770s bt2 index files: $VAR1 = []; 770s Note - bowtie-build indices do not yet exist. Indexing genome now. 770s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 770s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 770s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 770s 40 reads; of these: 770s 40 (100.00%) were unpaired; of these: 770s 0 (0.00%) aligned 0 times 770s 36 (90.00%) aligned exactly 1 time 770s 4 (10.00%) aligned >1 times 770s 100.00% overall alignment rate 770s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 770s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 770s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 770s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 771s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 771s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 771s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 771s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 771s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 771s 771s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 771s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 771s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 771s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 771s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 771s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 771s -processing jaccard pair sensor 771s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 771s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 771s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c21.trinity.reads.fa.out/inchworm.fa.clipped.fa 773s succeeded(22) 61.1111% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 773s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 773s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 773s bt2 index files: $VAR1 = []; 773s Note - bowtie-build indices do not yet exist. Indexing genome now. 773s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 773s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 773s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 774s 28 reads; of these: 774s 28 (100.00%) were unpaired; of these: 774s 0 (0.00%) aligned 0 times 774s 28 (100.00%) aligned exactly 1 time 774s 0 (0.00%) aligned >1 times 774s 100.00% overall alignment rate 774s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 774s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 774s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 774s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 774s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 774s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 774s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 774s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 774s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 774s 774s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 774s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 774s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 774s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 774s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 774s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 774s -processing jaccard pair sensor 774s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 774s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 774s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c7.trinity.reads.fa.out/inchworm.fa.clipped.fa 776s succeeded(23) 63.8889% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 776s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 776s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 776s bt2 index files: $VAR1 = []; 776s Note - bowtie-build indices do not yet exist. Indexing genome now. 776s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 777s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 777s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 777s 29 reads; of these: 777s 29 (100.00%) were unpaired; of these: 777s 0 (0.00%) aligned 0 times 777s 23 (79.31%) aligned exactly 1 time 777s 6 (20.69%) aligned >1 times 777s 100.00% overall alignment rate 777s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 777s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 777s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 777s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 777s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 777s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 777s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 777s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 777s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 777s 777s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 777s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 777s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 777s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 777s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 777s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 777s -processing jaccard pair sensor 777s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 777s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 777s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c12.trinity.reads.fa.out/inchworm.fa.clipped.fa 779s succeeded(24) 66.6667% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 779s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 779s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 779s bt2 index files: $VAR1 = []; 779s Note - bowtie-build indices do not yet exist. Indexing genome now. 779s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 779s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 779s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 780s 8 reads; of these: 780s 8 (100.00%) were unpaired; of these: 780s 0 (0.00%) aligned 0 times 780s 8 (100.00%) aligned exactly 1 time 780s 0 (0.00%) aligned >1 times 780s 100.00% overall alignment rate 780s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 780s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 780s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 780s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 780s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 780s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 780s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 780s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 780s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 780s 780s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 780s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 780s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 780s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 780s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 780s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 780s -processing jaccard pair sensor 780s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 780s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 780s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c14.trinity.reads.fa.out/inchworm.fa.clipped.fa 781s succeeded(25) 69.4444% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 781s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 781s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 781s bt2 index files: $VAR1 = []; 781s Note - bowtie-build indices do not yet exist. Indexing genome now. 781s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 781s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 781s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 782s 81 reads; of these: 782s 81 (100.00%) were unpaired; of these: 782s 0 (0.00%) aligned 0 times 782s 78 (96.30%) aligned exactly 1 time 782s 3 (3.70%) aligned >1 times 782s 100.00% overall alignment rate 782s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 782s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 782s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 782s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 782s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 782s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 782s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 782s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 782s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 782s 782s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 782s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 782s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 782s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 782s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 782s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 782s -processing jaccard pair sensor 782s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 782s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 782s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c20.trinity.reads.fa.out/inchworm.fa.clipped.fa 784s succeeded(26) 72.2222% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 784s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 784s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 784s bt2 index files: $VAR1 = []; 784s Note - bowtie-build indices do not yet exist. Indexing genome now. 784s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 785s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 785s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 785s 13 reads; of these: 785s 13 (100.00%) were unpaired; of these: 785s 0 (0.00%) aligned 0 times 785s 13 (100.00%) aligned exactly 1 time 785s 0 (0.00%) aligned >1 times 785s 100.00% overall alignment rate 785s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 785s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 785s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 785s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 785s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 785s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 785s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 785s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 785s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 785s 785s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 785s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 785s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 785s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 785s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 785s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 785s -processing jaccard pair sensor 785s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 785s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 785s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c27.trinity.reads.fa.out/inchworm.fa.clipped.fa 787s succeeded(27) 75% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 787s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 787s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 787s bt2 index files: $VAR1 = []; 787s Note - bowtie-build indices do not yet exist. Indexing genome now. 787s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 787s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 787s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 788s 1556 reads; of these: 788s 1556 (100.00%) were unpaired; of these: 788s 1 (0.06%) aligned 0 times 788s 1328 (85.35%) aligned exactly 1 time 788s 227 (14.59%) aligned >1 times 788s 99.94% overall alignment rate 788s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 788s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 788s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 788s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 788s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 788s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 788s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 788s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 788s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 788s 788s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 788s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 788s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 788s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 788s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 788s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 788s -processing jaccard pair sensor 788s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 788s [1000 lines read] scaff:a4;5 lend:109 rend:184 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 788s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c6.trinity.reads.fa.out/inchworm.fa.clipped.fa 792s succeeded(28) 77.7778% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 792s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 792s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 792s bt2 index files: $VAR1 = []; 792s Note - bowtie-build indices do not yet exist. Indexing genome now. 792s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 792s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 792s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 792s 20 reads; of these: 792s 20 (100.00%) were unpaired; of these: 792s 0 (0.00%) aligned 0 times 792s 20 (100.00%) aligned exactly 1 time 792s 0 (0.00%) aligned >1 times 792s 100.00% overall alignment rate 792s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 792s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 792s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 792s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 792s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 792s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 792s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 792s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 792s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 792s 792s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 792s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 792s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 792s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 792s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 792s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 792s -processing jaccard pair sensor 792s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 792s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 792s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c10.trinity.reads.fa.out/inchworm.fa.clipped.fa 795s succeeded(29) 80.5556% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 795s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 795s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 795s bt2 index files: $VAR1 = []; 795s Note - bowtie-build indices do not yet exist. Indexing genome now. 795s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 796s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 796s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 796s 8656 reads; of these: 796s 8656 (100.00%) were unpaired; of these: 796s 6 (0.07%) aligned 0 times 796s 5677 (65.58%) aligned exactly 1 time 796s 2973 (34.35%) aligned >1 times 796s 99.93% overall alignment rate 796s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 796s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 797s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 797s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 797s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam 797s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam 797s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 797s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam 797s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 797s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 797s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 797s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 797s 797s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 797s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 797s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 797s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 797s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 797s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 797s -processing jaccard pair sensor 798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 798s [1000 lines read] scaff:a1;61 lend:632 rend:881 [2000 lines read] scaff:a1;61 lend:2374 rend:2686 [3000 lines read] scaff:a1;61 lend:3935 rend:4312 [4000 lines read] scaff:a1;61 lend:5397 rend:5666 [5000 lines read] scaff:a1;61 lend:6299 rend:6522 [6000 lines read] scaff:a38;2 lend:1 rend:38 [7000 lines read] scaff:a53;2 lend:1 rend:33 [8000 lines read] scaff:a70;2 lend:1 rend:40 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c1.trinity.reads.fa.out/inchworm.fa.clipped.fa 805s succeeded(30) 83.3333% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 805s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 805s bt2 index files: $VAR1 = []; 805s Note - bowtie-build indices do not yet exist. Indexing genome now. 805s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 805s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 805s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 805s 9 reads; of these: 805s 9 (100.00%) were unpaired; of these: 805s 0 (0.00%) aligned 0 times 805s 9 (100.00%) aligned exactly 1 time 805s 0 (0.00%) aligned >1 times 805s 100.00% overall alignment rate 805s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 805s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 805s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 805s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 805s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 805s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 805s 805s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 805s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 805s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 805s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 805s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 805s -processing jaccard pair sensor 805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c30.trinity.reads.fa.out/inchworm.fa.clipped.fa 808s succeeded(31) 86.1111% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 808s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 808s bt2 index files: $VAR1 = []; 808s Note - bowtie-build indices do not yet exist. Indexing genome now. 808s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 808s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 808s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 808s 20 reads; of these: 808s 20 (100.00%) were unpaired; of these: 808s 0 (0.00%) aligned 0 times 808s 20 (100.00%) aligned exactly 1 time 808s 0 (0.00%) aligned >1 times 808s 100.00% overall alignment rate 808s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 808s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 808s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 808s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 808s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 808s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 808s 808s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 808s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 808s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 808s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 808s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 808s -processing jaccard pair sensor 808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c9.trinity.reads.fa.out/inchworm.fa.clipped.fa 810s succeeded(32) 88.8889% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 810s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 810s bt2 index files: $VAR1 = []; 810s Note - bowtie-build indices do not yet exist. Indexing genome now. 810s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 811s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 811s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 811s 11 reads; of these: 811s 11 (100.00%) were unpaired; of these: 811s 0 (0.00%) aligned 0 times 811s 11 (100.00%) aligned exactly 1 time 811s 0 (0.00%) aligned >1 times 811s 100.00% overall alignment rate 811s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 811s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 811s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 811s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 811s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 811s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 811s 811s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 811s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 811s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 811s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 811s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 811s -processing jaccard pair sensor 811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c13.trinity.reads.fa.out/inchworm.fa.clipped.fa 813s succeeded(33) 91.6667% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 813s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 813s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 813s bt2 index files: $VAR1 = []; 813s Note - bowtie-build indices do not yet exist. Indexing genome now. 813s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 813s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 813s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 814s 9 reads; of these: 814s 9 (100.00%) were unpaired; of these: 814s 0 (0.00%) aligned 0 times 814s 9 (100.00%) aligned exactly 1 time 814s 0 (0.00%) aligned >1 times 814s 100.00% overall alignment rate 814s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 814s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 814s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 814s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 814s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 814s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 814s 814s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 814s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 814s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 814s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 814s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 814s -processing jaccard pair sensor 814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c34.trinity.reads.fa.out/inchworm.fa.clipped.fa 818s succeeded(34) 94.4444% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 818s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 818s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 818s bt2 index files: $VAR1 = []; 818s Note - bowtie-build indices do not yet exist. Indexing genome now. 818s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 818s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 818s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 820s 11272 reads; of these: 820s 11272 (100.00%) were unpaired; of these: 820s 2 (0.02%) aligned 0 times 820s 1241 (11.01%) aligned exactly 1 time 820s 10029 (88.97%) aligned >1 times 820s 99.98% overall alignment rate 820s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 820s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 822s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 822s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 822s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam 822s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam 822s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 822s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam 822s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 822s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 822s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 822s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 822s 824s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 824s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 824s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 824s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 824s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 824s -processing jaccard pair sensor 826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 827s [1000 lines read] scaff:a107;3 lend:1 rend:45 [2000 lines read] scaff:a113;2 lend:1 rend:42 [3000 lines read] scaff:a118;2 lend:14 rend:59 [4000 lines read] scaff:a123;3 lend:1 rend:35 [5000 lines read] scaff:a131;2 lend:1 rend:44 [6000 lines read] scaff:a137;2 lend:1 rend:49 [7000 lines read] scaff:a144;2 lend:45 rend:84 [8000 lines read] scaff:a153;2 lend:7 rend:49 [9000 lines read] scaff:a162;2 lend:1 rend:46 [10000 lines read] scaff:a170;2 lend:3 rend:78 [11000 lines read] scaff:a175;2 lend:1 rend:49 [12000 lines read] scaff:a181;2 lend:26 rend:57 [13000 lines read] scaff:a187;2 lend:1 rend:41 [14000 lines read] scaff:a192;2 lend:8 rend:51 [15000 lines read] scaff:a198;2 lend:1 rend:49 [16000 lines read] scaff:a1;139 lend:291 rend:478 [17000 lines read] scaff:a1;139 lend:907 rend:1219 [18000 lines read] scaff:a1;139 lend:1602 rend:1915 [19000 lines read] scaff:a1;139 lend:2262 rend:2337 [20000 lines read] scaff:a1;139 lend:2817 rend:2946 [21000 lines read] scaff:a1;139 lend:3282 rend:3521 [22000 lines read] scaff:a205;2 lend:1 rend:40 [23000 lines read] scaff:a210;2 lend:1 rend:35 [24000 lines read] scaff:a221;2 lend:1 rend:49 [25000 lines read] scaff:a226;2 lend:3 rend:38 [26000 lines read] scaff:a235;2 lend:19 rend:60 [27000 lines read] scaff:a250;2 lend:1 rend:49 [28000 lines read] scaff:a258;2 lend:1 rend:35 [29000 lines read] scaff:a27;2 lend:77 rend:126 [30000 lines read] scaff:a36;4 lend:1 rend:47 [31000 lines read] scaff:a42;2 lend:1 rend:55 [32000 lines read] scaff:a51;2 lend:16 rend:91 [33000 lines read] scaff:a58;3 lend:1 rend:47 [34000 lines read] scaff:a62;2 lend:13 rend:43 [35000 lines read] scaff:a6;2 lend:4 rend:43 [36000 lines read] scaff:a76;2 lend:15 rend:57 [37000 lines read] scaff:a81;2 lend:20 rend:63 [38000 lines read] scaff:a8;5 lend:4 rend:52 [39000 lines read] scaff:a95;2 lend:1 rend:45 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 827s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c3.trinity.reads.fa.out/inchworm.fa.clipped.fa 834s succeeded(35) 97.2222% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 834s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa --CPU 2 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 834s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 834s bt2 index files: $VAR1 = []; 834s Note - bowtie-build indices do not yet exist. Indexing genome now. 834s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa 834s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 834s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 834s 18 reads; of these: 834s 18 (100.00%) were unpaired; of these: 834s 0 (0.00%) aligned 0 times 834s 18 (100.00%) aligned exactly 1 time 834s 0 (0.00%) aligned >1 times 834s 100.00% overall alignment rate 834s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 834s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 834s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 834s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 834s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 834s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 834s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 834s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 834s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 834s 834s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 834s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 834s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 834s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 834s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 834s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 834s -processing jaccard pair sensor 834s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 834s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 834s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c16.trinity.reads.fa.out/inchworm.fa.clipped.fa 836s succeeded(36) 100% completed. 836s 836s All commands completed successfully. :-) 836s 836s 836s 836s ** Harvesting all assembled transcripts into a single multi-fasta file... 836s 836s Saturday, November 2, 2024: 17:50:52 CMD: find /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/ -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/Trinity.tmp 836s * [Sat Nov 2 17:50:52 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa 1 838s * [Sat Nov 2 17:50:54 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta 838s Saturday, November 2, 2024: 17:50:54 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta.gene_trans_map 838s 838s 838s ############################################################################# 838s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta 838s ############################################################################# 838s 838s 838s ./misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh 838s 838s 838s exit 0 838s #!/bin/bash -ve 838s 838s 838s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then 838s gunzip -c reads.right.fq.gz > reads.right.fq 838s fi 838s 838s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then 838s gunzip -c reads.left.fq.gz > reads.left.fq 838s fi 838s 838s if [ -e reads2.right.fq.gz ] && [ ! -e reads2.right.fq ]; then 838s gunzip -c reads2.right.fq.gz > reads2.right.fq 838s fi 838s 838s if [ -e reads2.left.fq.gz ] && [ ! -e reads2.left.fq ]; then 838s gunzip -c reads2.left.fq.gz > reads2.left.fq 838s fi 838s 838s 838s ####################################################### 838s ## Run Trinity to Generate Transcriptome Assemblies ## 838s ####################################################### 838s 838s CPU=$(nproc || sysctl -n hw.physicalcpu) 838s 838s ${TRINITY_HOME}/Trinity --seqType fq \ 838s --max_memory 2G \ 838s --left reads.left.fq,reads2.left.fq \ 838s --right reads.right.fq,reads2.right.fq \ 838s --SS_lib_type RF \ 838s --CPU ${CPU} \ 838s --trimmomatic \ 838s --normalize_reads \ 838s --normalize_by_read_set \ 838s --output trinity_trim_and_norm_outdir 838s 838s 838s ______ ____ ____ ____ ____ ______ __ __ 838s | || \ | || \ | || || | | 838s | || D ) | | | _ | | | | || | | 838s |_| |_|| / | | | | | | | |_| |_|| ~ | 838s | | | \ | | | | | | | | | |___, | 838s | | | . \ | | | | | | | | | | | 838s |__| |__|\_||____||__|__||____| |__| |____/ 838s 838s Trinity-v2.15.1 838s 838s 838s 838s Left read files: $VAR1 = [ 838s 'reads.left.fq', 838s 'reads2.left.fq' 838s ]; 838s Right read files: $VAR1 = [ 838s 'reads.right.fq', 838s 'reads2.right.fq' 838s ]; 838s Saturday, November 2, 2024: 17:50:54 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir 838s Saturday, November 2, 2024: 17:50:54 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis 838s 838s 838s ---------------------------------------------------------------------------------- 838s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 838s ---------------------------------------------------------------------------------- 838s 838s --------------------------------------------------------------- 838s ------ Quality Trimming Via Trimmomatic --------------------- 838s << ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >> 838s --------------------------------------------------------------- 838s 838s 838s ## Running Trimmomatic on read files: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq, /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq 838s Saturday, November 2, 2024: 17:50:54 CMD: java -jar /usr/share/java/trimmomatic.jar PE -threads 2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 838s TrimmomaticPE: Started with arguments: 838s -threads 2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 838s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' 838s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences 838s Quality encoding detected as phred33 839s Input Read Pairs: 30575 Both Surviving: 27726 (90.68%) Forward Only Surviving: 746 (2.44%) Reverse Only Surviving: 722 (2.36%) Dropped: 1381 (4.52%) 839s TrimmomaticPE: Completed successfully 839s Saturday, November 2, 2024: 17:50:55 CMD: cp reads.left.fq.P.qtrim reads.left.fq.PwU.qtrim.fq 839s Saturday, November 2, 2024: 17:50:55 CMD: cp reads.right.fq.P.qtrim reads.right.fq.PwU.qtrim.fq 839s Saturday, November 2, 2024: 17:50:55 CMD: touch trimmomatic.ok 839s Saturday, November 2, 2024: 17:50:55 CMD: gzip reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim & 839s 839s ## Running Trimmomatic on read files: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq, /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq 839s Saturday, November 2, 2024: 17:50:55 CMD: java -jar /usr/share/java/trimmomatic.jar PE -threads 2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq reads2.left.fq.P.qtrim reads2.left.fq.U.qtrim reads2.right.fq.P.qtrim reads2.right.fq.U.qtrim ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 839s TrimmomaticPE: Started with arguments: 839s -threads 2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq reads2.left.fq.P.qtrim reads2.left.fq.U.qtrim reads2.right.fq.P.qtrim reads2.right.fq.U.qtrim ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 839s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' 839s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences 839s Quality encoding detected as phred33 840s Input Read Pairs: 30575 Both Surviving: 27726 (90.68%) Forward Only Surviving: 746 (2.44%) Reverse Only Surviving: 722 (2.36%) Dropped: 1381 (4.52%) 840s TrimmomaticPE: Completed successfully 840s Saturday, November 2, 2024: 17:50:56 CMD: cp reads2.left.fq.P.qtrim reads2.left.fq.PwU.qtrim.fq 840s Saturday, November 2, 2024: 17:50:56 CMD: cp reads2.right.fq.P.qtrim reads2.right.fq.PwU.qtrim.fq 840s Saturday, November 2, 2024: 17:50:56 CMD: touch trimmomatic.ok 840s Saturday, November 2, 2024: 17:50:56 CMD: gzip reads2.left.fq.P.qtrim reads2.left.fq.U.qtrim reads2.right.fq.P.qtrim reads2.right.fq.U.qtrim & 840s --------------------------------------------------------------- 840s ------------ In silico Read Normalization --------------------- 840s -- (Removing Excess Reads Beyond 200 Coverage -- 840s --------------------------------------------------------------- 840s 840s 840s ## Running in silico normalization, processing each read set separately 840s # running normalization on reads: $VAR1 = [ 840s [ 840s 'reads.left.fq.PwU.qtrim.fq' 840s ], 840s [ 840s 'reads.right.fq.PwU.qtrim.fq' 840s ] 840s ]; 840s 840s 840s Saturday, November 2, 2024: 17:50:56 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1 --max_CV 10000 --SS_lib_type RF --left reads.left.fq.PwU.qtrim.fq --right reads.right.fq.PwU.qtrim.fq --pairs_together --PARALLEL_STATS 840s -prepping seqs 840s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.left.fq.PwU.qtrim.fq >> left.fa 840s CMD: seqtk-trinity seq -A -R 2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.right.fq.PwU.qtrim.fq >> right.fa 840s CMD finished (0 seconds) 840s CMD finished (0 seconds) 840s CMD: touch left.fa.ok 840s CMD finished (0 seconds) 840s CMD: touch right.fa.ok 840s CMD finished (0 seconds) 840s Done converting input files.CMD: cat left.fa right.fa > both.fa 841s CMD finished (0 seconds) 841s CMD: touch both.fa.ok 841s CMD finished (0 seconds) 841s -kmer counting. 841s ------------------------------------------- 841s ----------- Jellyfish -------------------- 841s -- (building a k-mer catalog from reads) -- 841s ------------------------------------------- 841s 841s CMD: jellyfish count -t 2 -m 25 -s 100000000 both.fa 842s CMD finished (1 seconds) 842s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 842s CMD finished (0 seconds) 842s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 842s CMD finished (0 seconds) 842s CMD: touch jellyfish.K25.min2.kmers.fa.success 842s CMD finished (0 seconds) 842s -generating stats files 842s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > left.fa.K25.stats 842s -reading Kmer occurrences... 842s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > right.fa.K25.stats 842s -reading Kmer occurrences... 842s 842s done parsing 88153 Kmers, 88076 added, taking 0 seconds. 842s 842s done parsing 88153 Kmers, 88076 added, taking 0 seconds. 843s STATS_GENERATION_TIME: 1 seconds. 843s CMD finished (1 seconds) 843s STATS_GENERATION_TIME: 1 seconds. 843s CMD finished (1 seconds) 843s CMD: touch left.fa.K25.stats.ok 843s CMD finished (0 seconds) 843s CMD: touch right.fa.K25.stats.ok 843s CMD finished (0 seconds) 843s -sorting each stats file by read name. 843s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort 843s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort 843s CMD finished (0 seconds) 843s CMD finished (0 seconds) 843s CMD: touch left.fa.K25.stats.sort.ok 843s CMD finished (0 seconds) 843s CMD: touch right.fa.K25.stats.sort.ok 843s CMD finished (0 seconds) 843s -defining normalized reads 843s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats 843s -opening left.fa.K25.stats.sort 843s -opening right.fa.K25.stats.sort 843s -done opening files. 844s CMD finished (1 seconds) 844s CMD: touch pairs.K25.stats.ok 844s CMD finished (0 seconds) 844s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200 --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs 844s 27678 / 27726 = 99.83% reads selected during normalization. 844s 0 / 27726 = 0.00% reads discarded as likely aberrant based on coverage profiles. 844s 0 / 27726 = 0.00% reads discarded as below minimum coverage threshold=1 844s CMD finished (0 seconds) 844s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 844s CMD finished (0 seconds) 844s -search and capture. 845s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.right.fq.PwU.qtrim.fq ... done prepping, now search and capture. 845s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.right.fq.PwU.qtrim.fq 845s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.left.fq.PwU.qtrim.fq ... done prepping, now search and capture. 845s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.left.fq.PwU.qtrim.fq 845s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/reads.left.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 845s CMD finished (0 seconds) 845s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/reads.right.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 845s CMD finished (0 seconds) 845s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/reads.left.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq 845s CMD finished (0 seconds) 845s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/reads.right.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq 845s CMD finished (0 seconds) 845s -removing tmp dir /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/tmp_normalized_reads 845s 845s 845s Normalization complete. See outputs: 845s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/reads.left.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq 845s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/reads.right.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq 845s Saturday, November 2, 2024: 17:51:01 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/normalization.ok 845s # running normalization on reads: $VAR1 = [ 845s [ 845s 'reads2.left.fq.PwU.qtrim.fq' 845s ], 845s [ 845s 'reads2.right.fq.PwU.qtrim.fq' 845s ] 845s ]; 845s 845s 845s Saturday, November 2, 2024: 17:51:01 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2 --max_CV 10000 --SS_lib_type RF --left reads2.left.fq.PwU.qtrim.fq --right reads2.right.fq.PwU.qtrim.fq --pairs_together --PARALLEL_STATS 845s -prepping seqs 845s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.left.fq.PwU.qtrim.fq >> left.fa 845s CMD: seqtk-trinity seq -A -R 2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.right.fq.PwU.qtrim.fq >> right.fa 845s CMD finished (0 seconds) 845s CMD finished (0 seconds) 845s CMD: touch left.fa.ok 845s CMD finished (0 seconds) 845s CMD: touch right.fa.ok 845s CMD finished (0 seconds) 845s Done converting input files.CMD: cat left.fa right.fa > both.fa 845s CMD finished (0 seconds) 845s CMD: touch both.fa.ok 845s CMD finished (0 seconds) 845s -kmer counting. 845s ------------------------------------------- 845s ----------- Jellyfish -------------------- 845s -- (building a k-mer catalog from reads) -- 845s ------------------------------------------- 845s 845s CMD: jellyfish count -t 2 -m 25 -s 100000000 both.fa 846s CMD finished (1 seconds) 846s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 846s CMD finished (0 seconds) 846s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 846s CMD finished (0 seconds) 846s CMD: touch jellyfish.K25.min2.kmers.fa.success 846s CMD finished (0 seconds) 846s -generating stats files 846s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > left.fa.K25.stats 846s -reading Kmer occurrences... 846s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > right.fa.K25.stats 846s -reading Kmer occurrences... 847s 847s done parsing 88153 Kmers, 88076 added, taking 1 seconds. 847s 847s done parsing 88153 Kmers, 88076 added, taking 1 seconds. 847s STATS_GENERATION_TIME: 0 seconds. 847s STATS_GENERATION_TIME: 0 seconds. 847s CMD finished (1 seconds) 847s CMD finished (1 seconds) 847s CMD: touch left.fa.K25.stats.ok 847s CMD finished (0 seconds) 847s CMD: touch right.fa.K25.stats.ok 847s CMD finished (0 seconds) 847s -sorting each stats file by read name. 847s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort 847s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort 847s CMD finished (0 seconds) 847s CMD finished (0 seconds) 847s CMD: touch left.fa.K25.stats.sort.ok 847s CMD finished (0 seconds) 847s CMD: touch right.fa.K25.stats.sort.ok 847s CMD finished (0 seconds) 847s -defining normalized reads 847s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats 847s -opening left.fa.K25.stats.sort 847s -opening right.fa.K25.stats.sort 847s -done opening files. 848s CMD finished (1 seconds) 848s CMD: touch pairs.K25.stats.ok 848s CMD finished (0 seconds) 848s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200 --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs 848s 27678 / 27726 = 99.83% reads selected during normalization. 848s 0 / 27726 = 0.00% reads discarded as likely aberrant based on coverage profiles. 848s 0 / 27726 = 0.00% reads discarded as below minimum coverage threshold=1 848s CMD finished (0 seconds) 848s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 848s CMD finished (0 seconds) 848s -search and capture. 849s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.right.fq.PwU.qtrim.fq ... done prepping, now search and capture. 849s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.right.fq.PwU.qtrim.fq 849s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.left.fq.PwU.qtrim.fq ... done prepping, now search and capture. 849s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.left.fq.PwU.qtrim.fq 849s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/reads2.left.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 849s CMD finished (0 seconds) 849s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/reads2.right.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 849s CMD finished (0 seconds) 849s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/reads2.left.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq 849s CMD finished (0 seconds) 849s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/reads2.right.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq 849s CMD finished (0 seconds) 849s -removing tmp dir /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/tmp_normalized_reads 849s 849s 849s Normalization complete. See outputs: 849s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/reads2.left.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq 849s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/reads2.right.fq.PwU.qtrim.fq.normalized_K25_maxC200_minC1_maxCV10000.fq 849s Saturday, November 2, 2024: 17:51:05 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/normalization.ok 849s # running normalization on reads: $VAR1 = [ 849s [ 849s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq', 849s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq' 849s ], 849s [ 849s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq', 849s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq' 849s ] 849s ]; 849s 849s 849s Saturday, November 2, 2024: 17:51:05 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether --max_CV 10000 --SS_lib_type RF --left /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq,/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq --right /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq,/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq --pairs_together --PARALLEL_STATS 849s -prepping seqs 849s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq >> left.fa 849s CMD: seqtk-trinity seq -A -R 2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq >> right.fa 849s CMD finished (0 seconds) 849s CMD: seqtk-trinity seq -r -A -R 1 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq >> left.fa 849s CMD finished (0 seconds) 849s CMD: seqtk-trinity seq -A -R 2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq >> right.fa 849s CMD finished (0 seconds) 849s CMD finished (0 seconds) 849s CMD: touch left.fa.ok 849s CMD finished (0 seconds) 849s CMD: touch right.fa.ok 849s CMD finished (0 seconds) 849s Done converting input files.CMD: cat left.fa right.fa > both.fa 849s CMD finished (0 seconds) 849s CMD: touch both.fa.ok 849s CMD finished (0 seconds) 849s -kmer counting. 849s ------------------------------------------- 849s ----------- Jellyfish -------------------- 849s -- (building a k-mer catalog from reads) -- 849s ------------------------------------------- 849s 849s CMD: jellyfish count -t 2 -m 25 -s 100000000 both.fa 850s CMD finished (1 seconds) 850s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 850s CMD finished (0 seconds) 850s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 851s CMD finished (1 seconds) 851s CMD: touch jellyfish.K25.min2.kmers.fa.success 851s CMD finished (0 seconds) 851s -generating stats files 851s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > left.fa.K25.stats 851s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > right.fa.K25.stats 851s -reading Kmer occurrences... 851s -reading Kmer occurrences... 851s 851s done parsing 311705 Kmers, 310319 added, taking 0 seconds. 851s 851s done parsing 311705 Kmers, 310319 added, taking 0 seconds. 852s STATS_GENERATION_TIME: 1 seconds. 852s CMD finished (1 seconds) 852s STATS_GENERATION_TIME: 1 seconds. 852s CMD finished (1 seconds) 852s CMD: touch left.fa.K25.stats.ok 852s CMD finished (0 seconds) 852s CMD: touch right.fa.K25.stats.ok 852s CMD finished (0 seconds) 852s -sorting each stats file by read name. 852s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort 852s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort 852s CMD finished (0 seconds) 852s CMD finished (0 seconds) 852s CMD: touch left.fa.K25.stats.sort.ok 852s CMD finished (0 seconds) 852s CMD: touch right.fa.K25.stats.sort.ok 852s CMD finished (0 seconds) 852s -defining normalized reads 852s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats 852s -opening left.fa.K25.stats.sort 852s -opening right.fa.K25.stats.sort 852s -done opening files. 853s CMD finished (1 seconds) 853s CMD: touch pairs.K25.stats.ok 853s CMD finished (0 seconds) 853s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200 --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs 854s 51602 / 55356 = 93.22% reads selected during normalization. 854s 0 / 55356 = 0.00% reads discarded as likely aberrant based on coverage profiles. 854s 0 / 55356 = 0.00% reads discarded as below minimum coverage threshold=1 854s CMD finished (1 seconds) 854s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 854s CMD finished (0 seconds) 854s -search and capture. 856s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq ... done prepping, now search and capture. 856s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq 856s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq 856s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq ... done prepping, now search and capture. 856s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq 856s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq 856s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/left.norm.fq_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 856s CMD finished (0 seconds) 856s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/right.norm.fq_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 856s CMD finished (0 seconds) 856s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/left.norm.fq_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq 856s CMD finished (0 seconds) 856s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/right.norm.fq_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq 856s CMD finished (0 seconds) 856s -removing tmp dir /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/tmp_normalized_reads 856s 856s 856s Normalization complete. See outputs: 856s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/left.norm.fq_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq 856s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/right.norm.fq_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq 856s Saturday, November 2, 2024: 17:51:12 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/normalization.ok 856s Converting input files. (in parallel)Saturday, November 2, 2024: 17:51:12 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa 856s Saturday, November 2, 2024: 17:51:12 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa 856s Saturday, November 2, 2024: 17:51:12 CMD: touch left.fa.ok 856s Saturday, November 2, 2024: 17:51:12 CMD: touch right.fa.ok 856s Saturday, November 2, 2024: 17:51:12 CMD: touch left.fa.ok right.fa.ok 856s Saturday, November 2, 2024: 17:51:12 CMD: cat left.fa right.fa > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa 856s Saturday, November 2, 2024: 17:51:12 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa.ok 856s ------------------------------------------- 856s ----------- Jellyfish -------------------- 856s -- (building a k-mer (25) catalog from reads) -- 856s ------------------------------------------- 856s 856s * [Sat Nov 2 17:51:12 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa 858s * [Sat Nov 2 17:51:14 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 858s * [Sat Nov 2 17:51:14 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 858s ---------------------------------------------- 858s --------------- Inchworm (K=25, asm) --------------------- 858s -- (Linear contig construction from k-mers) -- 858s ---------------------------------------------- 858s 858s * [Sat Nov 2 17:51:14 2024] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --num_threads 2 --PARALLEL_IWORM --min_any_entropy 1.0 -L 25 --no_prune_error_kmers > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa.tmp 858s Kmer length set to: 25 858s Min assembly length set to: 25 858s Monitor turned on, set to: 1 858s min entropy set to: 1 858s setting number of threads to: 2 858s -setting parallel iworm mode. 858s -reading Kmer occurrences... 859s [0M] Kmers parsed. 859s done parsing 309493 Kmers, 309493 added, taking 1 seconds. 859s 859s TIMING KMER_DB_BUILDING 1 s. 859s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 859s Pruned 1482 kmers from catalog. 859s Pruning time: 0 seconds = 0 minutes. 859s 859s TIMING PRUNING 0 s. 859s -populating the kmer seed candidate list. 859s Kcounter hash size: 309493 859s Processed 308011 non-zero abundance kmers in kcounter. 859s -Not sorting list of kmers, given parallel mode in effect. 859s -beginning inchworm contig assembly. 859s Total kcounter hash size: 309493 vs. sorted list size: 308011 859s num threads set to: 2 859s Done opening file. tmp.iworm.fa.pid_44732.thread_0 859s Done opening file. tmp.iworm.fa.pid_44732.thread_1 860s 860s Iworm contig assembly time: 1 seconds = 0.0166667 minutes. 860s 860s TIMING CONTIG_BUILDING 1 s. 860s 860s TIMING PROG_RUNTIME 2 s. 860s * [Sat Nov 2 17:51:16 2024] Running CMD: mv /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa.tmp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa 860s Saturday, November 2, 2024: 17:51:16 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa.finished 860s -------------------------------------------------------- 860s -------------------- Chrysalis ------------------------- 860s -- (Contig Clustering & de Bruijn Graph Construction) -- 860s -------------------------------------------------------- 860s 860s inchworm_target: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa 860s bowtie_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa 860s chrysalis_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa 860s * [Sat Nov 2 17:51:16 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa 100 10 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 860s * [Sat Nov 2 17:51:16 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 1>/dev/null 860s * [Sat Nov 2 17:51:16 2024] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa | samtools view -@ 2 -F4 -Sb - | samtools sort -m 536870912 -@ 2 -no /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm.bowtie.nameSorted.bam" 869s * [Sat Nov 2 17:51:25 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_scaffolds.txt 870s * [Sat Nov 2 17:51:26 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48 -strand -scaffolding /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt 872s * [Sat Nov 2 17:51:28 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k9,9gr /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted 872s * [Sat Nov 2 17:51:28 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 872s * [Sat Nov 2 17:51:28 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 -weld_graph /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/GraphFromIwormFasta.out 872s * [Sat Nov 2 17:51:28 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/bundled_iworm_contigs.fasta -min 200 872s * [Sat Nov 2 17:51:28 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa -f /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -strand -p 10 876s * [Sat Nov 2 17:51:32 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/readsToComponents.out > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/readsToComponents.out.sort 876s Saturday, November 2, 2024: 17:51:32 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/read_partitions/Fb_0/CBin_0 876s Saturday, November 2, 2024: 17:51:32 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/partitioned_reads.files.list.ok 876s Saturday, November 2, 2024: 17:51:32 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --SS_lib_type F --seqType fa --trinity_complete --full_cleanup --no_salmon > recursive_trinity.cmds 876s Saturday, November 2, 2024: 17:51:32 CMD: touch recursive_trinity.cmds.ok 876s Saturday, November 2, 2024: 17:51:32 CMD: touch recursive_trinity.cmds.ok 876s 876s 876s -------------------------------------------------------------------------------- 876s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 876s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 876s -------------------------------------------------------------------------------- 876s 876s Saturday, November 2, 2024: 17:51:32 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 876s Number of Commands: 50 991s succeeded(1) 2% completed. succeeded(2) 4% completed. succeeded(3) 6% completed. succeeded(4) 8% completed. succeeded(5) 10% completed. succeeded(6) 12% completed. succeeded(7) 14% completed. succeeded(8) 16% completed. succeeded(9) 18% completed. succeeded(10) 20% completed. succeeded(11) 22% completed. succeeded(12) 24% completed. succeeded(13) 26% completed. succeeded(14) 28% completed. succeeded(15) 30% completed. succeeded(16) 32% completed. succeeded(17) 34% completed. succeeded(18) 36% completed. succeeded(19) 38% completed. succeeded(20) 40% completed. succeeded(21) 42% completed. succeeded(22) 44% completed. succeeded(23) 46% completed. succeeded(24) 48% completed. succeeded(25) 50% completed. succeeded(26) 52% completed. succeeded(27) 54% completed. succeeded(28) 56% completed. succeeded(29) 58% completed. succeeded(30) 60% completed. succeeded(31) 62% completed. succeeded(32) 64% completed. succeeded(33) 66% completed. succeeded(34) 68% completed. succeeded(35) 70% completed. succeeded(36) 72% completed. succeeded(37) 74% completed. succeeded(38) 76% completed. succeeded(39) 78% completed. succeeded(40) 80% completed. succeeded(41) 82% completed. succeeded(42) 84% completed. succeeded(43) 86% completed. succeeded(44) 88% completed. succeeded(45) 90% completed. succeeded(46) 92% completed. succeeded(47) 94% completed. succeeded(48) 96% completed. succeeded(49) 98% completed. succeeded(50) 100% completed. 991s 991s All commands completed successfully. :-) 991s 991s 991s 991s ** Harvesting all assembled transcripts into a single multi-fasta file... 991s 991s Saturday, November 2, 2024: 17:53:27 CMD: find /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/read_partitions/ -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/Trinity.tmp 991s * [Sat Nov 2 17:53:27 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa 2 993s * [Sat Nov 2 17:53:29 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta 993s Saturday, November 2, 2024: 17:53:29 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta.gene_trans_map 993s 993s 993s ############################################################################# 993s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta 993s ############################################################################# 993s 993s 993s 993s 993s 993s exit 0 993s ./misc_run_tests/__runMe_include_long_reads.sh 993s #!/bin/bash -ve 993s 993s ####################################################### 993s ## Run Trinity to Generate Transcriptome Assemblies ## 993s ####################################################### 993s 993s CPU=$(nproc || sysctl -n hw.physicalcpu) 993s 993s ${TRINITY_HOME}/Trinity --seqType fq \ 993s --max_memory 2G \ 993s --left reads.left.fq.gz \ 993s --right reads.right.fq.gz \ 993s --SS_lib_type RF \ 993s --CPU ${CPU} \ 993s --no_cleanup \ 993s --long_reads longReads.fa \ 993s --output test_trinity_long_reads 993s 993s 993s ______ ____ ____ ____ ____ ______ __ __ 993s | || \ | || \ | || || | | 993s | || D ) | | | _ | | | | || | | 993s |_| |_|| / | | | | | | | |_| |_|| ~ | 993s | | | \ | | | | | | | | | |___, | 993s | | | . \ | | | | | | | | | | | 993s |__| |__|\_||____||__|__||____| |__| |____/ 993s 993s Trinity-v2.15.1 993s 993s 993s 993s Left read files: $VAR1 = [ 993s 'reads.left.fq.gz' 993s ]; 993s Right read files: $VAR1 = [ 993s 'reads.right.fq.gz' 993s ]; 993s Saturday, November 2, 2024: 17:53:29 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads 993s Saturday, November 2, 2024: 17:53:29 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis 993s 993s 993s ---------------------------------------------------------------------------------- 993s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 993s ---------------------------------------------------------------------------------- 993s 993s --------------------------------------------------------------- 993s ------------ In silico Read Normalization --------------------- 993s -- (Removing Excess Reads Beyond 200 Coverage -- 993s --------------------------------------------------------------- 993s 993s # running normalization on reads: $VAR1 = [ 993s [ 993s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz' 993s ], 993s [ 993s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz' 993s ] 993s ]; 993s 993s 993s Saturday, November 2, 2024: 17:53:29 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization --max_CV 10000 --SS_lib_type RF --no_cleanup --left /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together --PARALLEL_STATS 993s -prepping seqs 993s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa 993s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa 993s CMD finished (0 seconds) 993s CMD finished (0 seconds) 993s CMD: touch left.fa.ok 993s CMD finished (0 seconds) 993s CMD: touch right.fa.ok 993s CMD finished (0 seconds) 993s Done converting input files.CMD: cat left.fa right.fa > both.fa 993s CMD finished (0 seconds) 993s CMD: touch both.fa.ok 993s CMD finished (0 seconds) 993s -kmer counting. 993s ------------------------------------------- 993s ----------- Jellyfish -------------------- 993s -- (building a k-mer catalog from reads) -- 993s ------------------------------------------- 993s 993s CMD: jellyfish count -t 2 -m 25 -s 100000000 both.fa 995s CMD finished (2 seconds) 995s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 995s CMD finished (0 seconds) 995s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 995s CMD finished (0 seconds) 995s CMD: touch jellyfish.K25.min2.kmers.fa.success 995s CMD finished (0 seconds) 995s -generating stats files 995s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > left.fa.K25.stats 995s -reading Kmer occurrences... 995s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > right.fa.K25.stats 995s -reading Kmer occurrences... 996s 996s done parsing 100973 Kmers, 100873 added, taking 1 seconds. 996s 996s done parsing 100973 Kmers, 100873 added, taking 1 seconds. 996s STATS_GENERATION_TIME: 0 seconds. 996s CMD finished (1 seconds) 996s STATS_GENERATION_TIME: 0 seconds. 996s CMD finished (1 seconds) 996s CMD: touch left.fa.K25.stats.ok 996s CMD finished (0 seconds) 996s CMD: touch right.fa.K25.stats.ok 996s CMD finished (0 seconds) 996s -sorting each stats file by read name. 996s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort 996s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort 996s CMD finished (0 seconds) 996s CMD finished (0 seconds) 996s CMD: touch left.fa.K25.stats.sort.ok 996s CMD finished (0 seconds) 996s CMD: touch right.fa.K25.stats.sort.ok 996s CMD finished (0 seconds) 996s -defining normalized reads 996s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats 996s -opening left.fa.K25.stats.sort 996s -opening right.fa.K25.stats.sort 996s -done opening files. 997s CMD finished (1 seconds) 997s CMD: touch pairs.K25.stats.ok 997s CMD finished (0 seconds) 997s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200 --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs 997s 30472 / 30575 = 99.66% reads selected during normalization. 997s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles. 997s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1 997s CMD finished (0 seconds) 997s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 997s CMD finished (1 seconds) 997s -search and capture. 998s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture. 998s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz 998s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture. 998s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz 998s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 998s CMD finished (0 seconds) 998s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 998s CMD finished (0 seconds) 998s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq 998s CMD finished (0 seconds) 998s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq 998s CMD finished (0 seconds) 998s 998s 998s Normalization complete. See outputs: 998s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq 998s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq 998s Saturday, November 2, 2024: 17:53:34 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/normalization.ok 998s Converting input files. (in parallel)Saturday, November 2, 2024: 17:53:34 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa 998s Saturday, November 2, 2024: 17:53:34 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa 998s Saturday, November 2, 2024: 17:53:34 CMD: touch left.fa.ok 998s Saturday, November 2, 2024: 17:53:35 CMD: touch right.fa.ok 998s Saturday, November 2, 2024: 17:53:35 CMD: touch left.fa.ok right.fa.ok 998s Saturday, November 2, 2024: 17:53:35 CMD: cat left.fa right.fa > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa 999s Saturday, November 2, 2024: 17:53:35 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.ok 999s Saturday, November 2, 2024: 17:53:35 CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR 999s Saturday, November 2, 2024: 17:53:35 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/longReads.fa | sed 's/>/>LR\$\|/' >> /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR 999s Saturday, November 2, 2024: 17:53:35 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR.ok 999s ------------------------------------------- 999s ----------- Jellyfish -------------------- 999s -- (building a k-mer (25) catalog from reads) -- 999s ------------------------------------------- 999s 999s * [Sat Nov 2 17:53:35 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa 1000s * [Sat Nov 2 17:53:36 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 1001s * [Sat Nov 2 17:53:37 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 1001s ---------------------------------------------- 1001s --------------- Inchworm (K=25, asm) --------------------- 1001s -- (Linear contig construction from k-mers) -- 1001s ---------------------------------------------- 1001s 1001s * [Sat Nov 2 17:53:37 2024] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --keep_tmp_files --num_threads 2 --PARALLEL_IWORM --min_any_entropy 1.0 -L 25 --no_prune_error_kmers > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa.tmp 1001s Kmer length set to: 25 1001s Min assembly length set to: 25 1001s Monitor turned on, set to: 1 1001s -retaining tmp files 1001s min entropy set to: 1 1001s setting number of threads to: 2 1001s -setting parallel iworm mode. 1001s -reading Kmer occurrences... 1001s [0M] Kmers parsed. [0M] Kmers parsed. 1001s done parsing 519541 Kmers, 519541 added, taking 0 seconds. 1001s 1001s TIMING KMER_DB_BUILDING 0 s. 1001s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 1001s Pruned 4252 kmers from catalog. 1001s Pruning time: 0 seconds = 0 minutes. 1001s 1001s TIMING PRUNING 0 s. 1001s -populating the kmer seed candidate list. 1001s Kcounter hash size: 519541 1002s Processed 515289 non-zero abundance kmers in kcounter. 1002s -Not sorting list of kmers, given parallel mode in effect. 1002s -beginning inchworm contig assembly. 1002s Total kcounter hash size: 519541 vs. sorted list size: 515289 1002s num threads set to: 2 1002s Done opening file. tmp.iworm.fa.pid_53524.thread_0 1002s Done opening file. tmp.iworm.fa.pid_53524.thread_1 1002s 1002s Iworm contig assembly time: 0 seconds = 0 minutes. 1002s 1002s TIMING CONTIG_BUILDING 0 s. 1002s 1002s TIMING PROG_RUNTIME 1 s. 1002s * [Sat Nov 2 17:53:38 2024] Running CMD: mv /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa.tmp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa 1002s Saturday, November 2, 2024: 17:53:38 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa.finished 1002s -------------------------------------------------------- 1002s -------------------- Chrysalis ------------------------- 1002s -- (Contig Clustering & de Bruijn Graph Construction) -- 1002s -------------------------------------------------------- 1002s 1002s inchworm_target: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa 1002s bowtie_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa 1002s chrysalis_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR 1002s * [Sat Nov 2 17:53:38 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa 100 10 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 1002s * [Sat Nov 2 17:53:38 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 1>/dev/null 1003s * [Sat Nov 2 17:53:39 2024] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa | samtools view -@ 2 -F4 -Sb - | samtools sort -m 536870912 -@ 2 -no /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm.bowtie.nameSorted.bam" 1007s * [Sat Nov 2 17:53:43 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_scaffolds.txt 1008s * [Sat Nov 2 17:53:44 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48 -strand -scaffolding /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt 1010s * [Sat Nov 2 17:53:47 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k9,9gr /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted 1011s * [Sat Nov 2 17:53:47 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 1011s * [Sat Nov 2 17:53:47 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 -weld_graph /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/GraphFromIwormFasta.out 1011s * [Sat Nov 2 17:53:47 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/bundled_iworm_contigs.fasta -min 200 1011s * [Sat Nov 2 17:53:47 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR -f /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -strand -p 10 1012s * [Sat Nov 2 17:53:49 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/readsToComponents.out > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/readsToComponents.out.sort 1013s Saturday, November 2, 2024: 17:53:49 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/read_partitions/Fb_0/CBin_0 1013s Saturday, November 2, 2024: 17:53:49 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/partitioned_reads.files.list.ok 1013s Saturday, November 2, 2024: 17:53:49 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --SS_lib_type F --seqType fa --trinity_complete --no_cleanup --long_reads_mode --no_salmon > recursive_trinity.cmds 1013s Saturday, November 2, 2024: 17:53:49 CMD: touch recursive_trinity.cmds.ok 1013s Saturday, November 2, 2024: 17:53:49 CMD: touch recursive_trinity.cmds.ok 1013s 1013s 1013s -------------------------------------------------------------------------------- 1013s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 1013s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 1013s -------------------------------------------------------------------------------- 1013s 1013s Saturday, November 2, 2024: 17:53:49 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 1013s Number of Commands: 39 1092s succeeded(1) 2.5641% completed. succeeded(2) 5.12821% completed. succeeded(3) 7.69231% completed. succeeded(4) 10.2564% completed. succeeded(5) 12.8205% completed. succeeded(6) 15.3846% completed. succeeded(7) 17.9487% completed. succeeded(8) 20.5128% completed. succeeded(9) 23.0769% completed. succeeded(10) 25.641% completed. succeeded(11) 28.2051% completed. succeeded(12) 30.7692% completed. succeeded(13) 33.3333% completed. succeeded(14) 35.8974% completed. succeeded(15) 38.4615% completed. succeeded(16) 41.0256% completed. succeeded(17) 43.5897% completed. succeeded(18) 46.1538% completed. succeeded(19) 48.7179% completed. succeeded(20) 51.2821% completed. succeeded(21) 53.8462% completed. succeeded(22) 56.4103% completed. succeeded(23) 58.9744% completed. succeeded(24) 61.5385% completed. succeeded(25) 64.1026% completed. succeeded(26) 66.6667% completed. succeeded(27) 69.2308% completed. succeeded(28) 71.7949% completed. succeeded(29) 74.359% completed. succeeded(30) 76.9231% completed. succeeded(31) 79.4872% completed. succeeded(32) 82.0513% completed. succeeded(33) 84.6154% completed. succeeded(34) 87.1795% completed. succeeded(35) 89.7436% completed. succeeded(36) 92.3077% completed. succeeded(37) 94.8718% completed. succeeded(38) 97.4359% completed. succeeded(39) 100% completed. 1092s 1092s All commands completed successfully. :-) 1092s 1092s 1092s 1092s ** Harvesting all assembled transcripts into a single multi-fasta file... 1092s 1092s Saturday, November 2, 2024: 17:55:08 CMD: find /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/read_partitions/ -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/Trinity.tmp 1092s * [Sat Nov 2 17:55:08 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa 2 1093s * [Sat Nov 2 17:55:09 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta 1093s Saturday, November 2, 2024: 17:55:09 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta.gene_trans_map 1093s 1093s 1093s ############################################################################# 1093s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta 1093s ############################################################################# 1093s 1093s 1093s 1093s 1093s find test_trinity_long_reads/ -regex ".*allProbPaths.fasta" -exec cat {} \; | grep LR 1093s >c0_g1_i1 len=6205 path=[1:0-1805 1784:1806-1822 1801:1823-5597 5576:5598-5738 5717:5739-5739 5718:5740-6173 6152:6174-6203 7380:6204-6204] [-1, 1, 1784, 1801, 5576, 5717, 5718, 6152, 7380, -2] long_read_mappings: {PairPath [_paths=[[1, 1784, 1801, 5576, 5717, 5718], []]]=[LR$|mm9chr1-NM_001102430;mm9chr1-211673_Arfgef1_ADP-ribosylation_factor_guanine_mm9chr1:10128913-10222575(-)]} 1093s >c0_g1_i2 len=6219 path=[1:0-1805 1784:1806-1822 1801:1823-5597 5576:5598-5738 5717:5739-5739 5718:5740-6173 7351:6174-6177 7355:6178-6178 7445:6179-6218] [-1, 1, 1784, 1801, 5576, 5717, 5718, 7351, 7355, 7445, -2] long_read_mappings: {PairPath [_paths=[[1, 1784, 1801, 5576, 5717, 5718], []]]=[LR$|mm9chr1-NM_001102430;mm9chr1-211673_Arfgef1_ADP-ribosylation_factor_guanine_mm9chr1:10128913-10222575(-)]} 1093s >c0_g1_i6 len=7194 path=[1:0-1805 1784:1806-1822 1801:1823-5597 5576:5598-5738 5717:5739-5739 5718:5740-6173 6152:6174-6203 6182:6204-6219 6198:6220-6729 6708:6730-6733 6712:6734-6735 6714:6736-7193] [-1, 1, 1784, 1801, 5576, 5717, 5718, 6152, 6182, 6198, 6708, 6712, 6714, -2] long_read_mappings: {PairPath [_paths=[[1, 1784, 1801, 5576, 5717, 5718], []]]=[LR$|mm9chr1-NM_001102430;mm9chr1-211673_Arfgef1_ADP-ribosylation_factor_guanine_mm9chr1:10128913-10222575(-)]} 1093s >c0_g1_i3 len=2433 path=[1:0-610 589:611-1077 2766:1078-1168 1078:1169-1610 1520:1611-1690 1600:1691-1863 1773:1864-2097 2007:2098-2098 2008:2099-2432] [-1, 1, 589, 2766, 1078, 1520, 1600, 1773, 2007, 2008, -2] long_read_mappings: {PairPath [_paths=[[1, 589, 2766, 1078, 1520, 1600, 1773, 2007, 2008], []]]=[LR$|mm9chr6-NM_022332;mm9chr6-64213_St7_low_density_lipoprotein-related_protein_12_mm9chr6:17699593-17892765(+)]} 1093s >c0_g1_i5 len=2364 path=[1:0-610 589:611-1077 1056:1078-1099 1078:1100-1541 1520:1542-1621 1600:1622-1794 1773:1795-2028 2007:2029-2029 2008:2030-2363] [-1, 1, 589, 1056, 1078, 1520, 1600, 1773, 2007, 2008, -2] long_read_mappings: {PairPath [_paths=[[1, 589, 1056, 1078, 1520, 1600, 1773, 2007, 2008], []]]=[LR$|mm9chr6-NM_001083315;mm9chr6-64213_St7_low_density_lipoprotein-related_protein_12_mm9chr6:17699593-17892765(+)]} 1093s >c0_g1_i1 len=2118 path=[2641:0-65 2684:66-412 3031:413-413 8119:414-436 3114:437-2097 8302:2098-2117] [-1, 2641, 2684, 3031, 8119, 3114, 8302, -2] long_read_mappings: {PairPath [_paths=[[3114], []]]=[LR$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]} 1093s >c0_g1_i2 len=2177 path=[2641:0-65 2684:66-412 3031:413-413 3032:414-495 3114:496-2156 8302:2157-2176] [-1, 2641, 2684, 3031, 3032, 3114, 8302, -2] long_read_mappings: {PairPath [_paths=[[3114], []]]=[LR$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]} 1093s >c0_g1_i3 len=5435 path=[2641:0-65 2684:66-412 3031:413-413 8119:414-436 3114:437-2097 4775:2098-3844 6522:3845-3860 6538:3861-4938 7616:4939-4939 7617:4940-4976 7616:4977-4977 7654:4978-5434] [-1, 2641, 2684, 3031, 8119, 3114, 4775, 6522, 6538, 7616, 7617, 7616, 7654, -2] long_read_mappings: {PairPath [_paths=[[3114], []]]=[LR$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]} 1093s >c0_g1_i4 len=5494 path=[2641:0-65 2684:66-412 3031:413-413 3032:414-495 3114:496-2156 4775:2157-3903 6522:3904-3919 6538:3920-4997 7616:4998-4998 7617:4999-5035 7616:5036-5036 7654:5037-5493] [-1, 2641, 2684, 3031, 3032, 3114, 4775, 6522, 6538, 7616, 7617, 7616, 7654, -2] long_read_mappings: {PairPath [_paths=[[3114], []]]=[LR$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]} 1093s >c0_g3_i2 len=3966 path=[5835:0-165 147:166-1345 5978:1346-1417 1348:1418-1418 7191:1419-1442 1373:1443-1489 1420:1490-1490 1421:1491-1650 1581:1651-2963 2894:2964-3730 6074:3731-3965] [-1, 5835, 147, 5978, 1348, 7191, 1373, 1420, 1421, 1581, 2894, 6074, -2] long_read_mappings: {PairPath [_paths=[[147, 5978, 1348, 7191, 1373, 1420, 1421, 1581, 2894, 6074], []]]=[LR$|mm9chr7-NM_022979;mm9chr7-269966_Nup98_nucleoporin_98_mm9chr7:109283074-109344374(-)]} 1093s >c0_g1_i4 len=8757 path=[1:0-333 312:334-1874 1853:1875-2722 2701:2723-3436 3415:3437-4380 4359:4381-6645 6624:6646-6646 6625:6647-6661 6640:6662-6662 6641:6663-7161 7140:7162-7164 7143:7165-7182 7161:7183-7208 7187:7209-7239 7218:7240-7240 7219:7241-7260 7239:7261-7261 11404:7262-7285 7264:7286-7623 7602:7624-7968 7947:7969-7969 7948:7970-7982 7961:7983-7983 7962:7984-8252 8231:8253-8747 8726:8748-8756] [-1, 1, 312, 1853, 2701, 3415, 4359, 6624, 6625, 6640, 6641, 7140, 7143, 7161, 7187, 7218, 7219, 7239, 11404, 7264, 7602, 7947, 7948, 7961, 7962, 8231, 8726, -2] long_read_mappings: {PairPath [_paths=[[1, 312, 1853, 2701, 3415, 4359, 6624, 6625, 6640, 6641, 7140, 7143, 7161, 7187, 7218, 7219, 7239, 11404, 7264], []]]=[LR$|mm9chr2-NM_153125;mm9chr2-227648_Sec16a_SEC16_homolog_A_mm9chr2:26266405-26297521(-)]} 1093s >c0_g1_i6 len=7669 path=[1:0-333 312:334-1874 1853:1875-2722 2701:2723-3436 3415:3437-4380 4359:4381-6645 6624:6646-6646 6625:6647-6661 6640:6662-6662 6641:6663-7161 7140:7162-7164 7143:7165-7182 7161:7183-7208 7187:7209-7239 7218:7240-7240 7219:7241-7260 7239:7261-7261 11404:7262-7285 7264:7286-7623 8735:7624-7668] [-1, 1, 312, 1853, 2701, 3415, 4359, 6624, 6625, 6640, 6641, 7140, 7143, 7161, 7187, 7218, 7219, 7239, 11404, 7264, 8735, -2] long_read_mappings: {PairPath [_paths=[[1, 312, 1853, 2701, 3415, 4359, 6624, 6625, 6640, 6641, 7140, 7143, 7161, 7187, 7218, 7219, 7239, 11404, 7264], []]]=[LR$|mm9chr2-NM_153125;mm9chr2-227648_Sec16a_SEC16_homolog_A_mm9chr2:26266405-26297521(-)]} 1093s >c0_g1_i2 len=1946 path=[1:0-219 198:220-220 199:221-304 283:305-325 304:326-1945] [-1, 1, 198, 199, 283, 304, -2] long_read_mappings: {PairPath [_paths=[[1, 198, 199, 283, 304], []]]=[LR$|mm9chr9-NM_026942;mm9chr9-69106_Stoml1_stomatin-like_1_mm9chr9:58101074-58109646(+)]} 1093s >c0_g1_i7 len=2514 path=[1:0-1204 1183:1205-1226 1205:1227-1649 1628:1650-1650 6231:1651-1674 1653:1675-2040 2019:2041-2041 2020:2042-2063 2042:2064-2227 2206:2228-2248 2227:2249-2513] [-1, 1, 1183, 1205, 1628, 6231, 1653, 2019, 2020, 2042, 2206, 2227, -2] long_read_mappings: {PairPath [_paths=[[1, 1183, 1205, 1628, 6231, 1653, 2019, 2020, 2042], []]]=[LR$|mm9chr8-NM_027590;mm9chr8-70885_Ints10_integrator_complex_subunit_10_mm9chr8:71317919-71351332(+)]} 1093s >c0_g1_i16 len=2273 path=[1:0-1204 1183:1205-1226 1205:1227-1649 1628:1650-1650 6231:1651-1674 1653:1675-2040 2019:2041-2041 2020:2042-2063 2042:2064-2227 2206:2228-2248 6207:2249-2272] [-1, 1, 1183, 1205, 1628, 6231, 1653, 2019, 2020, 2042, 2206, 6207, -2] long_read_mappings: {PairPath [_paths=[[1, 1183, 1205, 1628, 6231, 1653, 2019, 2020, 2042], []]]=[LR$|mm9chr8-NM_027590;mm9chr8-70885_Ints10_integrator_complex_subunit_10_mm9chr8:71317919-71351332(+)]} 1093s >c0_g1_i1 len=3823 path=[1:0-2158 2137:2159-2410 2389:2411-3822] [-1, 1, 2137, 2389, -2] long_read_mappings: {PairPath [_paths=[[1, 2137, 2389], []]]=[LR$|mm9chr2-NM_033134;mm9chr2-64436_Inpp5e_inositol_polyphosphate-5-phosphatase_E_mm9chr2:26253359-26264107(-)]} 1093s >c0_g1_i2 len=4179 path=[1:0-1751 1730:1752-1773 1752:1774-2693 2672:2694-4164 5684:4165-4178] [-1, 1, 1730, 1752, 2672, 5684, -2] long_read_mappings: {PairPath [_paths=[[1, 1730, 1752, 2672], []]]=[LR$|mm9chr5-NM_172722;mm9chr5-231713_Naa25_Nalpha_acteyltransferase_25_mm9chr5:121848014-121889959(+)]} 1093s >c0_g1_i5 len=5399 path=[1:0-1751 1730:1752-1773 1752:1774-2693 2672:2694-4164 4143:4165-5398] [-1, 1, 1730, 1752, 2672, 4143, -2] long_read_mappings: {PairPath [_paths=[[1, 1730, 1752, 2672], []]]=[LR$|mm9chr5-NM_172722;mm9chr5-231713_Naa25_Nalpha_acteyltransferase_25_mm9chr5:121848014-121889959(+)]} 1093s >c0_g1_i2 len=3739 path=[1:0-286 265:287-289 268:290-399 3806:400-459 396:460-3738] [-1, 1, 265, 268, 3806, 396, -2] long_read_mappings: {PairPath [_paths=[[268, 3806, 396], []]]=[LR$|mm9chr4-NM_010598;mm9chr4-16498_Kcnab2_potassium_voltage-gated_channel,_shaker-related_mm9chr4:151767144-151809990(-)]} 1093s >c0_g1_i3 len=3590 path=[3675:0-117 3770:118-137 265:138-140 268:141-250 3806:251-310 396:311-3589] [-1, 3675, 3770, 265, 268, 3806, 396, -2] long_read_mappings: {PairPath [_paths=[[268, 3806, 396], []]]=[LR$|mm9chr4- 1093s 1093s exit 0 1093s NM_010598;mm9chr4-16498_Kcnab2_potassium_voltage-gated_channel,_shaker-related_mm9chr4:151767144-151809990(-)]} 1093s ./misc_run_tests/__run_PE_samples_file.sh 1093s #!/bin/bash -ve 1093s 1093s ${TRINITY_HOME}/Trinity --samples_file samples.PE.txt \ 1093s --seqType fq \ 1093s --max_memory 1G \ 1093s --output trinity_test_samples_PE 1093s 1093s 1093s ______ ____ ____ ____ ____ ______ __ __ 1093s | || \ | || \ | || || | | 1093s | || D ) | | | _ | | | | || | | 1093s |_| |_|| / | | | | | | | |_| |_|| ~ | 1093s | | | \ | | | | | | | | | |___, | 1093s | | | . \ | | | | | | | | | | | 1093s |__| |__|\_||____||__|__||____| |__| |____/ 1093s 1093s Trinity-v2.15.1 1093s 1093s 1093s 1093s Left read files: $VAR1 = [ 1093s 'reads.left.fq.gz', 1093s 'reads2.left.fq.gz' 1093s ]; 1093s Right read files: $VAR1 = [ 1093s 'reads.right.fq.gz', 1093s 'reads2.right.fq.gz' 1093s ]; 1093s Saturday, November 2, 2024: 17:55:09 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE 1093s Saturday, November 2, 2024: 17:55:10 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis 1094s 1094s 1094s ---------------------------------------------------------------------------------- 1094s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1094s ---------------------------------------------------------------------------------- 1094s 1094s --------------------------------------------------------------- 1094s ------------ In silico Read Normalization --------------------- 1094s -- (Removing Excess Reads Beyond 200 Coverage -- 1094s --------------------------------------------------------------- 1094s 1094s # running normalization on reads: $VAR1 = [ 1094s [ 1094s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz', 1094s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz' 1094s ], 1094s [ 1094s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz', 1094s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz' 1094s ] 1094s ]; 1094s 1094s 1094s Saturday, November 2, 2024: 17:55:10 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization --max_CV 10000 --left /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz --right /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz,/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz --pairs_together --PARALLEL_STATS 1094s -prepping seqs 1094s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa 1094s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa 1094s CMD finished (0 seconds) 1094s CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz) >> left.fa 1094s CMD finished (0 seconds) 1094s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz) >> right.fa 1094s CMD finished (0 seconds) 1094s CMD finished (0 seconds) 1094s CMD: touch left.fa.ok 1094s CMD finished (0 seconds) 1094s CMD: touch right.fa.ok 1094s CMD finished (0 seconds) 1094s Done converting input files.CMD: cat left.fa right.fa > both.fa 1094s CMD finished (0 seconds) 1094s CMD: touch both.fa.ok 1094s CMD finished (0 seconds) 1094s -kmer counting. 1094s ------------------------------------------- 1094s ----------- Jellyfish -------------------- 1094s -- (building a k-mer catalog from reads) -- 1094s ------------------------------------------- 1094s 1094s CMD: jellyfish count -t 2 -m 25 -s 100000000 --canonical both.fa 1096s CMD finished (2 seconds) 1096s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 1096s CMD finished (0 seconds) 1096s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 1096s CMD finished (0 seconds) 1096s CMD: touch jellyfish.K25.min2.kmers.fa.success 1096s CMD finished (0 seconds) 1096s -generating stats files 1096s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 --DS > left.fa.K25.stats 1096s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 --DS > right.fa.K25.stats 1096s -reading Kmer occurrences... 1096s -reading Kmer occurrences... 1097s 1097s done parsing 518514 Kmers, 518514 added, taking 1 seconds. 1097s 1097s done parsing 518514 Kmers, 518514 added, taking 1 seconds. 1099s STATS_GENERATION_TIME: 2 seconds. 1099s STATS_GENERATION_TIME: 2 seconds. 1099s CMD finished (3 seconds) 1099s CMD finished (3 seconds) 1099s CMD: touch left.fa.K25.stats.ok 1099s CMD finished (0 seconds) 1099s CMD: touch right.fa.K25.stats.ok 1099s CMD finished (0 seconds) 1099s -sorting each stats file by read name. 1099s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort 1099s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort 1099s CMD finished (0 seconds) 1099s CMD finished (0 seconds) 1099s CMD: touch left.fa.K25.stats.sort.ok 1099s CMD finished (0 seconds) 1099s CMD: touch right.fa.K25.stats.sort.ok 1099s CMD finished (0 seconds) 1099s -defining normalized reads 1099s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats 1099s -opening left.fa.K25.stats.sort 1099s -opening right.fa.K25.stats.sort 1099s -done opening files. 1100s CMD finished (1 seconds) 1100s CMD: touch pairs.K25.stats.ok 1100s CMD finished (0 seconds) 1100s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200 --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs 1101s 56508 / 61150 = 92.41% reads selected during normalization. 1101s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles. 1101s 0 / 61150 = 0.00% reads discarded as below minimum coverage threshold=1 1101s CMD finished (1 seconds) 1101s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 1101s CMD finished (0 seconds) 1101s -search and capture. 1101s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz ... done prepping, now search and capture. 1101s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz 1101s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz ... done prepping, now search and capture. 1101s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz 1101s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz 1101s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz 1102s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 1102s CMD finished (0 seconds) 1102s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/reads.right.fq.gz_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 1102s CMD finished (0 seconds) 1102s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq 1102s CMD finished (0 seconds) 1102s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/reads.right.fq.gz_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq 1102s CMD finished (0 seconds) 1102s -removing tmp dir /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/tmp_normalized_reads 1102s 1102s 1102s Normalization complete. See outputs: 1102s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq 1102s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/reads.right.fq.gz_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq 1102s Saturday, November 2, 2024: 17:55:18 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/normalization.ok 1102s Converting input files. (in parallel)Saturday, November 2, 2024: 17:55:18 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -A -R 1 - >> left.fa 1102s Saturday, November 2, 2024: 17:55:18 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa 1102s Saturday, November 2, 2024: 17:55:18 CMD: touch left.fa.ok 1102s Saturday, November 2, 2024: 17:55:18 CMD: touch right.fa.ok 1102s Saturday, November 2, 2024: 17:55:19 CMD: touch left.fa.ok right.fa.ok 1102s Saturday, November 2, 2024: 17:55:19 CMD: cat left.fa right.fa > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa 1103s Saturday, November 2, 2024: 17:55:19 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa.ok 1103s ------------------------------------------- 1103s ----------- Jellyfish -------------------- 1103s -- (building a k-mer (25) catalog from reads) -- 1103s ------------------------------------------- 1103s 1103s * [Sat Nov 2 17:55:19 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa 1105s * [Sat Nov 2 17:55:21 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 1105s * [Sat Nov 2 17:55:21 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 1105s ---------------------------------------------- 1105s --------------- Inchworm (K=25, asm) --------------------- 1105s -- (Linear contig construction from k-mers) -- 1105s ---------------------------------------------- 1105s 1105s * [Sat Nov 2 17:55:21 2024] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --DS --num_threads 2 --PARALLEL_IWORM --min_any_entropy 1.0 -L 25 --no_prune_error_kmers > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa.tmp 1105s Kmer length set to: 25 1105s Min assembly length set to: 25 1105s Monitor turned on, set to: 1 1105s double stranded mode set 1105s min entropy set to: 1 1105s setting number of threads to: 2 1105s -setting parallel iworm mode. 1105s -reading Kmer occurrences... 1106s [0M] Kmers parsed. [0M] Kmers parsed. 1106s done parsing 515206 Kmers, 515206 added, taking 1 seconds. 1106s 1106s TIMING KMER_DB_BUILDING 1 s. 1106s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 1106s Pruned 4139 kmers from catalog. 1106s Pruning time: 0 seconds = 0 minutes. 1106s 1106s TIMING PRUNING 0 s. 1106s -populating the kmer seed candidate list. 1106s Kcounter hash size: 515206 1106s Processed 511067 non-zero abundance kmers in kcounter. 1106s -Not sorting list of kmers, given parallel mode in effect. 1106s -beginning inchworm contig assembly. 1106s Total kcounter hash size: 515206 vs. sorted list size: 511067 1106s num threads set to: 2 1106s Done opening file. tmp.iworm.fa.pid_60696.thread_0 1106s Done opening file. tmp.iworm.fa.pid_60696.thread_1 1108s 1108s Iworm contig assembly time: 2 seconds = 0.0333333 minutes. 1108s 1108s TIMING CONTIG_BUILDING 2 s. 1108s 1108s TIMING PROG_RUNTIME 3 s. 1108s * [Sat Nov 2 17:55:24 2024] Running CMD: mv /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa.tmp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa 1108s Saturday, November 2, 2024: 17:55:24 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa.finished 1108s -------------------------------------------------------- 1108s -------------------- Chrysalis ------------------------- 1108s -- (Contig Clustering & de Bruijn Graph Construction) -- 1108s -------------------------------------------------------- 1108s 1108s inchworm_target: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa 1108s bowtie_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa 1108s chrysalis_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa 1108s * [Sat Nov 2 17:55:24 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa 100 10 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 1108s * [Sat Nov 2 17:55:24 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 1>/dev/null 1109s * [Sat Nov 2 17:55:25 2024] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa | samtools view -@ 2 -F4 -Sb - | samtools sort -m 268435456 -@ 2 -no /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm.bowtie.nameSorted.bam" 1119s * [Sat Nov 2 17:55:35 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_scaffolds.txt 1121s * [Sat Nov 2 17:55:37 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48 -scaffolding /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt 1125s * [Sat Nov 2 17:55:41 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k9,9gr /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted 1125s * [Sat Nov 2 17:55:41 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 1125s * [Sat Nov 2 17:55:41 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 -weld_graph /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/GraphFromIwormFasta.out 1125s * [Sat Nov 2 17:55:41 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/bundled_iworm_contigs.fasta -min 200 1125s * [Sat Nov 2 17:55:41 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa -f /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -p 10 1134s * [Sat Nov 2 17:55:50 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/readsToComponents.out > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/readsToComponents.out.sort 1134s Saturday, November 2, 2024: 17:55:50 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/read_partitions/Fb_0/CBin_0 1134s Saturday, November 2, 2024: 17:55:50 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/partitioned_reads.files.list.ok 1134s Saturday, November 2, 2024: 17:55:50 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --full_cleanup --no_salmon > recursive_trinity.cmds 1134s Saturday, November 2, 2024: 17:55:50 CMD: touch recursive_trinity.cmds.ok 1134s Saturday, November 2, 2024: 17:55:50 CMD: touch recursive_trinity.cmds.ok 1134s 1134s 1134s -------------------------------------------------------------------------------- 1134s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 1134s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 1134s -------------------------------------------------------------------------------- 1134s 1134s Saturday, November 2, 2024: 17:55:50 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 1134s Number of Commands: 61 1281s succeeded(1) 1.63934% completed. succeeded(2) 3.27869% completed. succeeded(3) 4.91803% completed. succeeded(4) 6.55738% completed. succeeded(5) 8.19672% completed. succeeded(6) 9.83607% completed. succeeded(7) 11.4754% completed. succeeded(8) 13.1148% completed. succeeded(9) 14.7541% completed. succeeded(10) 16.3934% completed. succeeded(11) 18.0328% completed. succeeded(12) 19.6721% completed. succeeded(13) 21.3115% completed. succeeded(14) 22.9508% completed. succeeded(15) 24.5902% completed. succeeded(16) 26.2295% completed. succeeded(17) 27.8689% completed. succeeded(18) 29.5082% completed. succeeded(19) 31.1475% completed. succeeded(20) 32.7869% completed. succeeded(21) 34.4262% completed. succeeded(22) 36.0656% completed. succeeded(23) 37.7049% completed. succeeded(24) 39.3443% completed. succeeded(25) 40.9836% completed. succeeded(26) 42.623% completed. succeeded(27) 44.2623% completed. succeeded(28) 45.9016% completed. succeeded(29) 47.541% completed. succeeded(30) 49.1803% completed. succeeded(31) 50.8197% completed. succeeded(32) 52.459% completed. succeeded(33) 54.0984% completed. succeeded(34) 55.7377% completed. succeeded(35) 57.377% completed. succeeded(36) 59.0164% completed. succeeded(37) 60.6557% completed. succeeded(38) 62.2951% completed. succeeded(39) 63.9344% completed. succeeded(40) 65.5738% completed. succeeded(41) 67.2131% completed. succeeded(42) 68.8525% completed. succeeded(43) 70.4918% completed. succeeded(44) 72.1311% completed. succeeded(45) 73.7705% completed. succeeded(46) 75.4098% completed. succeeded(47) 77.0492% completed. succeeded(48) 78.6885% completed. succeeded(49) 80.3279% completed. succeeded(50) 81.9672% completed. succeeded(51) 83.6066% completed. succeeded(52) 85.2459% completed. succeeded(53) 86.8852% completed. succeeded(54) 88.5246% completed. succeeded(55) 90.1639% completed. succeeded(56) 91.8033% completed. succeeded(57) 93.4426% completed. succeeded(58) 95.082% completed. succeeded(59) 96.7213% completed. succeeded(60) 98.3607% completed. succeeded(61) 100% completed. 1281s 1281s All commands completed successfully. :-) 1281s 1281s 1281s 1281s ** Harvesting all assembled transcripts into a single multi-fasta file... 1281s 1281s Saturday, November 2, 2024: 17:58:17 CMD: find /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/read_partitions/ -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/Trinity.tmp 1281s * [Sat Nov 2 17:58:17 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa 2 1282s * [Sat Nov 2 17:58:18 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta 1282s Saturday, November 2, 2024: 17:58:18 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta.gene_trans_map 1282s 1282s 1282s ############################################################################# 1282s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta 1282s ############################################################################# 1282s 1282s 1282s 1282s ./misc_run_tests/__run_SE_samples_file.sh 1282s exit 0 1282s #!/bin/bash -ve 1282s 1282s ${TRINITY_HOME}/Trinity --samples_file samples.SE.txt \ 1282s --seqType fq \ 1282s --max_memory 1G \ 1282s --output trinity_test_samples_SE 1283s 1283s 1283s ______ ____ ____ ____ ____ ______ __ __ 1283s | || \ | || \ | || || | | 1283s | || D ) | | | _ | | | | || | | 1283s |_| |_|| / | | | | | | | |_| |_|| ~ | 1283s | | | \ | | | | | | | | | |___, | 1283s | | | . \ | | | | | | | | | | | 1283s |__| |__|\_||____||__|__||____| |__| |____/ 1283s 1283s Trinity-v2.15.1 1283s 1283s 1283s 1283s Single read files: $VAR1 = [ 1283s 'reads.left.fq.gz', 1283s 'reads2.left.fq.gz' 1283s ]; 1283s Saturday, November 2, 2024: 17:58:19 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE 1283s Saturday, November 2, 2024: 17:58:19 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis 1283s 1283s 1283s ---------------------------------------------------------------------------------- 1283s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1283s ---------------------------------------------------------------------------------- 1283s 1283s --------------------------------------------------------------- 1283s ------------ In silico Read Normalization --------------------- 1283s -- (Removing Excess Reads Beyond 200 Coverage -- 1283s --------------------------------------------------------------- 1283s 1283s # running normalization on reads: $VAR1 = [ 1283s [ 1283s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz', 1283s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz' 1283s ] 1283s ]; 1283s 1283s 1283s Saturday, November 2, 2024: 17:58:19 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization --max_CV 10000 --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz 1283s -prepping seqs 1283s CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> single.fa 1283s CMD finished (0 seconds) 1283s CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz) >> single.fa 1283s CMD finished (0 seconds) 1283s CMD: touch single.fa.ok 1283s CMD finished (0 seconds) 1283s -kmer counting. 1283s ------------------------------------------- 1283s ----------- Jellyfish -------------------- 1283s -- (building a k-mer catalog from reads) -- 1283s ------------------------------------------- 1283s 1283s CMD: jellyfish count -t 2 -m 25 -s 100000000 --canonical single.fa 1285s CMD finished (2 seconds) 1285s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 1285s CMD finished (0 seconds) 1285s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 1285s CMD finished (0 seconds) 1285s CMD: touch jellyfish.K25.min2.kmers.fa.success 1285s CMD finished (0 seconds) 1285s -generating stats files 1285s CMD: /usr/bin/fastaToKmerCoverageStats --reads single.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 2 --DS > single.fa.K25.stats 1285s -reading Kmer occurrences... 1285s 1285s done parsing 288470 Kmers, 288470 added, taking 0 seconds. 1286s STATS_GENERATION_TIME: 1 seconds. 1286s CMD finished (1 seconds) 1286s CMD: touch single.fa.K25.stats.ok 1286s CMD finished (0 seconds) 1286s -sorting each stats file by read name. 1286s CMD: head -n1 single.fa.K25.stats > single.fa.K25.stats.sort && tail -n +2 single.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> single.fa.K25.stats.sort 1286s CMD finished (0 seconds) 1286s CMD: touch single.fa.K25.stats.sort.ok 1286s CMD finished (0 seconds) 1286s -defining normalized reads 1286s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file single.fa.K25.stats.sort --max_cov 200 --min_cov 1 --max_CV 10000 > single.fa.K25.stats.sort.maxC200.minC1.maxCV10000.accs 1286s 59311 / 61150 = 96.99% reads selected during normalization. 1286s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles. 1286s 0 / 61150 = 0.00% reads discarded as below minimum coverage threshold=1 1286s CMD finished (1 seconds) 1287s CMD: touch single.fa.K25.stats.sort.maxC200.minC1.maxCV10000.accs.ok 1287s CMD finished (0 seconds) 1287s -search and capture. 1287s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz ... done prepping, now search and capture. 1287s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz 1287s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz 1288s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 1288s CMD finished (0 seconds) 1288s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq single.norm.fq 1288s CMD finished (0 seconds) 1288s -removing tmp dir /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/tmp_normalized_reads 1288s 1288s 1288s Normalization complete. See outputs: 1288s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq 1288s Saturday, November 2, 2024: 17:58:24 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/normalization.ok 1288s Saturday, November 2, 2024: 17:58:24 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/single.norm.fq | seqtk-trinity seq -A -R 1 - >> single.fa 1288s Saturday, November 2, 2024: 17:58:24 CMD: touch single.fa.ok 1288s Saturday, November 2, 2024: 17:58:24 CMD: touch single.fa.ok 1288s ------------------------------------------- 1288s ----------- Jellyfish -------------------- 1288s -- (building a k-mer (25) catalog from reads) -- 1288s ------------------------------------------- 1288s 1288s * [Sat Nov 2 17:58:24 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa 1290s * [Sat Nov 2 17:58:26 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 1290s * [Sat Nov 2 17:58:26 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 1290s ---------------------------------------------- 1290s --------------- Inchworm (K=25, asm) --------------------- 1290s -- (Linear contig construction from k-mers) -- 1290s ---------------------------------------------- 1290s 1290s * [Sat Nov 2 17:58:26 2024] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --DS --num_threads 2 --PARALLEL_IWORM --min_any_entropy 1.0 -L 25 --no_prune_error_kmers > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa.tmp 1290s Kmer length set to: 25 1290s Min assembly length set to: 25 1290s Monitor turned on, set to: 1 1290s double stranded mode set 1290s min entropy set to: 1 1290s setting number of threads to: 2 1290s -setting parallel iworm mode. 1290s -reading Kmer occurrences... 1290s [0M] Kmers parsed. 1290s done parsing 287930 Kmers, 287930 added, taking 0 seconds. 1290s 1290s TIMING KMER_DB_BUILDING 0 s. 1290s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 1290s Pruned 2078 kmers from catalog. 1290s Pruning time: 0 seconds = 0 minutes. 1290s 1290s TIMING PRUNING 0 s. 1290s -populating the kmer seed candidate list. 1290s Kcounter hash size: 287930 1290s Processed 285852 non-zero abundance kmers in kcounter. 1290s -Not sorting list of kmers, given parallel mode in effect. 1290s -beginning inchworm contig assembly. 1290s Total kcounter hash size: 287930 vs. sorted list size: 285852 1290s num threads set to: 2 1290s Done opening file. tmp.iworm.fa.pid_70906.thread_0 1290s Done opening file. tmp.iworm.fa.pid_70906.thread_1 1291s 1291s Iworm contig assembly time: 1 seconds = 0.0166667 minutes. 1291s 1291s TIMING CONTIG_BUILDING 1 s. 1291s 1291s TIMING PROG_RUNTIME 1 s. 1291s * [Sat Nov 2 17:58:27 2024] Running CMD: mv /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa.tmp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa 1291s Saturday, November 2, 2024: 17:58:27 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa.finished 1291s -------------------------------------------------------- 1291s -------------------- Chrysalis ------------------------- 1291s -- (Contig Clustering & de Bruijn Graph Construction) -- 1291s -------------------------------------------------------- 1291s 1291s inchworm_target: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa 1291s bowtie_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa 1291s chrysalis_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa 1291s * [Sat Nov 2 17:58:27 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa 100 10 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100 1292s * [Sat Nov 2 17:58:28 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt 1297s * [Sat Nov 2 17:58:33 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k9,9gr /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted 1297s * [Sat Nov 2 17:58:33 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 1297s * [Sat Nov 2 17:58:33 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100 -weld_graph /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/GraphFromIwormFasta.out 1297s * [Sat Nov 2 17:58:33 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/bundled_iworm_contigs.fasta -min 200 1297s * [Sat Nov 2 17:58:33 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa -f /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -p 10 1301s * [Sat Nov 2 17:58:37 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/readsToComponents.out > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/readsToComponents.out.sort 1301s Saturday, November 2, 2024: 17:58:37 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/read_partitions/Fb_0/CBin_0 1301s Saturday, November 2, 2024: 17:58:37 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/partitioned_reads.files.list.ok 1301s Saturday, November 2, 2024: 17:58:37 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/partitioned_reads.files.list --CPU 1 --max_memory 1G --seqType fa --trinity_complete --full_cleanup --no_salmon > recursive_trinity.cmds 1301s Saturday, November 2, 2024: 17:58:37 CMD: touch recursive_trinity.cmds.ok 1301s Saturday, November 2, 2024: 17:58:37 CMD: touch recursive_trinity.cmds.ok 1301s 1301s 1301s -------------------------------------------------------------------------------- 1301s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 1301s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 1301s -------------------------------------------------------------------------------- 1301s 1301s Saturday, November 2, 2024: 17:58:37 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 1301s Number of Commands: 45 1382s succeeded(1) 2.22222% completed. succeeded(2) 4.44444% completed. succeeded(3) 6.66667% completed. succeeded(4) 8.88889% completed. succeeded(5) 11.1111% completed. succeeded(6) 13.3333% completed. succeeded(7) 15.5556% completed. succeeded(8) 17.7778% completed. succeeded(9) 20% completed. succeeded(10) 22.2222% completed. succeeded(11) 24.4444% completed. succeeded(12) 26.6667% completed. succeeded(13) 28.8889% completed. succeeded(14) 31.1111% completed. succeeded(15) 33.3333% completed. succeeded(16) 35.5556% completed. succeeded(17) 37.7778% completed. succeeded(18) 40% completed. succeeded(19) 42.2222% completed. succeeded(20) 44.4444% completed. succeeded(21) 46.6667% completed. succeeded(22) 48.8889% completed. succeeded(23) 51.1111% completed. succeeded(24) 53.3333% completed. succeeded(25) 55.5556% completed. succeeded(26) 57.7778% completed. succeeded(27) 60% completed. succeeded(28) 62.2222% completed. succeeded(29) 64.4444% completed. succeeded(30) 66.6667% completed. succeeded(31) 68.8889% completed. succeeded(32) 71.1111% completed. succeeded(33) 73.3333% completed. succeeded(34) 75.5556% completed. succeeded(35) 77.7778% completed. succeeded(36) 80% completed. succeeded(37) 82.2222% completed. succeeded(38) 84.4444% completed. succeeded(39) 86.6667% completed. succeeded(40) 88.8889% completed. succeeded(41) 91.1111% completed. succeeded(42) 93.3333% completed. succeeded(43) 95.5556% completed. succeeded(44) 97.7778% completed. succeeded(45) 100% completed. 1382s 1382s All commands completed successfully. :-) 1382s 1382s 1382s 1382s ** Harvesting all assembled transcripts into a single multi-fasta file... 1382s 1382s Saturday, November 2, 2024: 17:59:58 CMD: find /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/read_partitions/ -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/Trinity.tmp 1382s * [Sat Nov 2 17:59:58 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa 2 1383s * [Sat Nov 2 17:59:59 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta 1383s Saturday, November 2, 2024: 18:00:00 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta.gene_trans_map 1383s 1383s 1383s ############################################################################# 1383s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta 1383s ############################################################################# 1383s 1383s 1384s ./misc_run_tests/__runMe_use_workdir.sh 1384s 1384s 1384s exit 0 1384s #!/bin/bash -ve 1384s 1384s 1384s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then 1384s gunzip -c reads.right.fq.gz > reads.right.fq 1384s fi 1384s 1384s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then 1384s gunzip -c reads.left.fq.gz > reads.left.fq 1384s fi 1384s 1384s 1384s 1384s ####################################################### 1384s ## Run Trinity to Generate Transcriptome Assemblies ## 1384s ####################################################### 1384s 1384s CPU=$(nproc || sysctl -n hw.physicalcpu) 1384s 1384s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \ 1384s --left reads.left.fq \ 1384s --right reads.right.fq \ 1384s --SS_lib_type RF \ 1384s --CPU ${CPU}\ 1384s --output trinity_with_workdir \ 1384s --workdir /tmp/trinity.workdir.$$ --full_cleanup 1384s 1384s 1384s ______ ____ ____ ____ ____ ______ __ __ 1384s | || \ | || \ | || || | | 1384s | || D ) | | | _ | | | | || | | 1384s |_| |_|| / | | | | | | | |_| |_|| ~ | 1384s | | | \ | | | | | | | | | |___, | 1384s | | | . \ | | | | | | | | | | | 1384s |__| |__|\_||____||__|__||____| |__| |____/ 1384s 1384s Trinity-v2.15.1 1384s 1384s 1384s 1384s Left read files: $VAR1 = [ 1384s 'reads.left.fq' 1384s ]; 1384s Right read files: $VAR1 = [ 1384s 'reads.right.fq' 1384s ]; 1384s Saturday, November 2, 2024: 18:00:00 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir 1384s Saturday, November 2, 2024: 18:00:00 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis 1384s 1384s 1384s ---------------------------------------------------------------------------------- 1384s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1384s ---------------------------------------------------------------------------------- 1384s 1384s --------------------------------------------------------------- 1384s ------------ In silico Read Normalization --------------------- 1384s -- (Removing Excess Reads Beyond 200 Coverage -- 1384s --------------------------------------------------------------- 1384s 1384s # running normalization on reads: $VAR1 = [ 1384s [ 1384s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq' 1384s ], 1384s [ 1384s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq' 1384s ] 1384s ]; 1384s 1384s 1384s Saturday, November 2, 2024: 18:00:00 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization --max_CV 10000 --SS_lib_type RF --left /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq --right /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq --pairs_together --PARALLEL_STATS 1384s -prepping seqs 1384s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq >> left.fa 1384s CMD: seqtk-trinity seq -A -R 2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq >> right.fa 1384s CMD finished (0 seconds) 1384s CMD finished (0 seconds) 1384s CMD: touch left.fa.ok 1384s CMD finished (0 seconds) 1384s CMD: touch right.fa.ok 1384s CMD finished (0 seconds) 1384s Done converting input files.CMD: cat left.fa right.fa > both.fa 1384s CMD finished (0 seconds) 1384s CMD: touch both.fa.ok 1384s CMD finished (0 seconds) 1384s -kmer counting. 1384s ------------------------------------------- 1384s ----------- Jellyfish -------------------- 1384s -- (building a k-mer catalog from reads) -- 1384s ------------------------------------------- 1384s 1384s CMD: jellyfish count -t 2 -m 25 -s 100000000 both.fa 1385s CMD finished (1 seconds) 1385s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 1385s CMD finished (0 seconds) 1385s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 1385s CMD finished (0 seconds) 1385s CMD: touch jellyfish.K25.min2.kmers.fa.success 1385s CMD finished (0 seconds) 1385s -generating stats files 1385s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > left.fa.K25.stats 1385s -reading Kmer occurrences... 1385s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 > right.fa.K25.stats 1385s -reading Kmer occurrences... 1386s 1386s done parsing 100973 Kmers, 100873 added, taking 1 seconds. 1386s 1386s done parsing 100973 Kmers, 100873 added, taking 1 seconds. 1386s STATS_GENERATION_TIME: 0 seconds. 1386s CMD finished (1 seconds) 1386s STATS_GENERATION_TIME: 0 seconds. 1386s CMD finished (1 seconds) 1386s CMD: touch left.fa.K25.stats.ok 1386s CMD finished (0 seconds) 1386s CMD: touch right.fa.K25.stats.ok 1386s CMD finished (0 seconds) 1386s -sorting each stats file by read name. 1386s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort 1386s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort 1386s CMD finished (0 seconds) 1386s CMD finished (0 seconds) 1386s CMD: touch left.fa.K25.stats.sort.ok 1386s CMD finished (0 seconds) 1386s CMD: touch right.fa.K25.stats.sort.ok 1386s CMD finished (0 seconds) 1386s -defining normalized reads 1386s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats 1386s -opening left.fa.K25.stats.sort 1386s -opening right.fa.K25.stats.sort 1386s -done opening files. 1387s CMD finished (1 seconds) 1387s CMD: touch pairs.K25.stats.ok 1387s CMD finished (0 seconds) 1387s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200 --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs 1387s 30472 / 30575 = 99.66% reads selected during normalization. 1387s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles. 1387s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1 1387s CMD finished (0 seconds) 1387s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 1387s CMD finished (0 seconds) 1387s -search and capture. 1388s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq ... done prepping, now search and capture. 1388s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq 1388s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq ... done prepping, now search and capture. 1388s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq 1388s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.left.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 1388s CMD finished (0 seconds) 1388s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.right.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 1388s CMD finished (0 seconds) 1388s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.left.fq.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq 1388s CMD finished (0 seconds) 1388s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.right.fq.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq 1388s CMD finished (0 seconds) 1388s -removing tmp dir /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/tmp_normalized_reads 1388s 1388s 1388s Normalization complete. See outputs: 1388s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.left.fq.normalized_K25_maxC200_minC1_maxCV10000.fq 1388s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.right.fq.normalized_K25_maxC200_minC1_maxCV10000.fq 1388s Saturday, November 2, 2024: 18:00:04 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/normalization.ok 1388s Converting input files. (in parallel)Saturday, November 2, 2024: 18:00:04 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa 1388s Saturday, November 2, 2024: 18:00:04 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa 1388s Saturday, November 2, 2024: 18:00:04 CMD: touch left.fa.ok 1388s Saturday, November 2, 2024: 18:00:04 CMD: touch right.fa.ok 1388s Saturday, November 2, 2024: 18:00:04 CMD: touch left.fa.ok right.fa.ok 1388s Saturday, November 2, 2024: 18:00:04 CMD: cat left.fa right.fa > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa 1388s Saturday, November 2, 2024: 18:00:04 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa.ok 1388s ------------------------------------------- 1388s ----------- Jellyfish -------------------- 1388s -- (building a k-mer (25) catalog from reads) -- 1388s ------------------------------------------- 1388s 1388s * [Sat Nov 2 18:00:04 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa 1390s * [Sat Nov 2 18:00:06 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 1390s * [Sat Nov 2 18:00:06 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 1390s ---------------------------------------------- 1390s --------------- Inchworm (K=25, asm) --------------------- 1390s -- (Linear contig construction from k-mers) -- 1390s ---------------------------------------------- 1390s 1390s * [Sat Nov 2 18:00:06 2024] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --num_threads 2 --PARALLEL_IWORM --min_any_entropy 1.0 -L 25 --no_prune_error_kmers > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa.tmp 1390s Kmer length set to: 25 1390s Min assembly length set to: 25 1390s Monitor turned on, set to: 1 1390s min entropy set to: 1 1390s setting number of threads to: 2 1390s -setting parallel iworm mode. 1390s -reading Kmer occurrences... 1391s [0M] Kmers parsed. [0M] Kmers parsed. 1391s done parsing 519541 Kmers, 519541 added, taking 1 seconds. 1391s 1391s TIMING KMER_DB_BUILDING 1 s. 1391s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 1391s Pruned 4252 kmers from catalog. 1391s Pruning time: 0 seconds = 0 minutes. 1391s 1391s TIMING PRUNING 0 s. 1391s -populating the kmer seed candidate list. 1391s Kcounter hash size: 519541 1391s Processed 515289 non-zero abundance kmers in kcounter. 1391s -Not sorting list of kmers, given parallel mode in effect. 1391s -beginning inchworm contig assembly. 1391s Total kcounter hash size: 519541 vs. sorted list size: 515289 1391s num threads set to: 2 1391s Done opening file. tmp.iworm.fa.pid_77807.thread_0 1391s Done opening file. tmp.iworm.fa.pid_77807.thread_1 1392s 1392s Iworm contig assembly time: 1 seconds = 0.0166667 minutes. 1392s 1392s TIMING CONTIG_BUILDING 1 s. 1392s 1392s TIMING PROG_RUNTIME 2 s. 1392s * [Sat Nov 2 18:00:08 2024] Running CMD: mv /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa.tmp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa 1392s Saturday, November 2, 2024: 18:00:08 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa.finished 1392s -------------------------------------------------------- 1392s -------------------- Chrysalis ------------------------- 1392s -- (Contig Clustering & de Bruijn Graph Construction) -- 1392s -------------------------------------------------------- 1392s 1392s inchworm_target: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa 1392s bowtie_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa 1392s chrysalis_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa 1392s * [Sat Nov 2 18:00:08 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa 100 10 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 1392s * [Sat Nov 2 18:00:08 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 1>/dev/null 1393s * [Sat Nov 2 18:00:09 2024] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa | samtools view -@ 2 -F4 -Sb - | samtools sort -m 536870912 -@ 2 -no /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm.bowtie.nameSorted.bam" 1398s * [Sat Nov 2 18:00:14 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_scaffolds.txt 1399s * [Sat Nov 2 18:00:15 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48 -strand -scaffolding /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt 1401s * [Sat Nov 2 18:00:17 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k9,9gr /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted 1401s * [Sat Nov 2 18:00:17 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 1401s * [Sat Nov 2 18:00:17 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 -weld_graph /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/GraphFromIwormFasta.out 1401s * [Sat Nov 2 18:00:17 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/bundled_iworm_contigs.fasta -min 200 1401s * [Sat Nov 2 18:00:17 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa -f /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -strand -p 10 1404s * [Sat Nov 2 18:00:20 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/readsToComponents.out > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/readsToComponents.out.sort 1404s Saturday, November 2, 2024: 18:00:20 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/read_partitions/Fb_0/CBin_0 1404s Saturday, November 2, 2024: 18:00:20 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/partitioned_reads.files.list.ok 1404s Saturday, November 2, 2024: 18:00:20 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --SS_lib_type F --seqType fa --trinity_complete --full_cleanup --workdir /tmp/trinity.workdir.77668 --no_salmon > recursive_trinity.cmds 1404s Saturday, November 2, 2024: 18:00:20 CMD: touch recursive_trinity.cmds.ok 1404s Saturday, November 2, 2024: 18:00:20 CMD: touch recursive_trinity.cmds.ok 1404s 1404s 1404s -------------------------------------------------------------------------------- 1404s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 1404s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 1404s -------------------------------------------------------------------------------- 1404s 1404s Saturday, November 2, 2024: 18:00:20 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 1404s Number of Commands: 39 1489s succeeded(1) 2.5641% completed. succeeded(2) 5.12821% completed. succeeded(3) 7.69231% completed. succeeded(4) 10.2564% completed. succeeded(5) 12.8205% completed. succeeded(6) 15.3846% completed. succeeded(7) 17.9487% completed. succeeded(8) 20.5128% completed. succeeded(9) 23.0769% completed. succeeded(10) 25.641% completed. succeeded(11) 28.2051% completed. succeeded(12) 30.7692% completed. succeeded(13) 33.3333% completed. succeeded(14) 35.8974% completed. succeeded(15) 38.4615% completed. succeeded(16) 41.0256% completed. succeeded(17) 43.5897% completed. succeeded(18) 46.1538% completed. succeeded(19) 48.7179% completed. succeeded(20) 51.2821% completed. succeeded(21) 53.8462% completed. succeeded(22) 56.4103% completed. succeeded(23) 58.9744% completed. succeeded(24) 61.5385% completed. succeeded(25) 64.1026% completed. succeeded(26) 66.6667% completed. succeeded(27) 69.2308% completed. succeeded(28) 71.7949% completed. succeeded(29) 74.359% completed. succeeded(30) 76.9231% completed. succeeded(31) 79.4872% completed. succeeded(32) 82.0513% completed. succeeded(33) 84.6154% completed. succeeded(34) 87.1795% completed. succeeded(35) 89.7436% completed. succeeded(36) 92.3077% completed. succeeded(37) 94.8718% completed. succeeded(38) 97.4359% completed. succeeded(39) 100% completed. 1489s 1489s All commands completed successfully. :-) 1489s 1489s 1489s 1489s ** Harvesting all assembled transcripts into a single multi-fasta file... 1489s 1489s Saturday, November 2, 2024: 18:01:45 CMD: find /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/read_partitions/ -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/Trinity.tmp 1489s * [Sat Nov 2 18:01:45 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa 2 1490s * [Sat Nov 2 18:01:46 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta 1490s 1490s 1490s ############################################################################# 1490s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta 1490s ############################################################################# 1490s 1490s 1490s Saturday, November 2, 2024: 18:01:46 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta.gene_trans_map 1490s 1490s 1490s exit 0 1490s ./misc_run_tests/__runMe_piecemeal.sh 1490s #!/bin/bash -ve 1490s 1490s ####################################################### 1490s ## Run Trinity to Generate Transcriptome Assemblies ## 1490s ####################################################### 1490s 1490s CPU=$(nproc || sysctl -n hw.physicalcpu) 1490s 1490s # stop before inchworm (just in silico norm) 1490s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU ${CPU} --output trinity_piecemeal --no_run_inchworm 1491s 1491s 1491s ______ ____ ____ ____ ____ ______ __ __ 1491s | || \ | || \ | || || | | 1491s | || D ) | | | _ | | | | || | | 1491s |_| |_|| / | | | | | | | |_| |_|| ~ | 1491s | | | \ | | | | | | | | | |___, | 1491s | | | . \ | | | | | | | | | | | 1491s |__| |__|\_||____||__|__||____| |__| |____/ 1491s 1491s Trinity-v2.15.1 1491s 1491s 1491s 1491s Left read files: $VAR1 = [ 1491s 'reads.left.fq.gz' 1491s ]; 1491s Right read files: $VAR1 = [ 1491s 'reads.right.fq.gz' 1491s ]; 1491s Saturday, November 2, 2024: 18:01:47 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal 1491s Saturday, November 2, 2024: 18:01:47 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis 1491s 1491s 1491s ---------------------------------------------------------------------------------- 1491s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1491s ---------------------------------------------------------------------------------- 1491s 1491s --------------------------------------------------------------- 1491s ------------ In silico Read Normalization --------------------- 1491s -- (Removing Excess Reads Beyond 200 Coverage -- 1491s --------------------------------------------------------------- 1491s 1491s # running normalization on reads: $VAR1 = [ 1491s [ 1491s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz' 1491s ], 1491s [ 1491s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz' 1491s ] 1491s ]; 1491s 1491s 1491s Saturday, November 2, 2024: 18:01:47 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization --max_CV 10000 --left /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together --PARALLEL_STATS 1491s -prepping seqs 1491s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa 1491s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa 1491s CMD finished (0 seconds) 1491s CMD finished (0 seconds) 1491s CMD: touch left.fa.ok 1491s CMD finished (0 seconds) 1491s CMD: touch right.fa.ok 1491s CMD finished (0 seconds) 1491s Done converting input files.CMD: cat left.fa right.fa > both.fa 1491s CMD finished (0 seconds) 1491s CMD: touch both.fa.ok 1491s CMD finished (0 seconds) 1491s -kmer counting. 1491s ------------------------------------------- 1491s ----------- Jellyfish -------------------- 1491s -- (building a k-mer catalog from reads) -- 1491s ------------------------------------------- 1491s 1491s CMD: jellyfish count -t 2 -m 25 -s 100000000 --canonical both.fa 1493s CMD finished (2 seconds) 1493s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 1493s CMD finished (0 seconds) 1493s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 1493s CMD finished (0 seconds) 1493s CMD: touch jellyfish.K25.min2.kmers.fa.success 1493s CMD finished (0 seconds) 1493s -generating stats files 1493s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 --DS > left.fa.K25.stats 1493s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 --DS > right.fa.K25.stats 1493s -reading Kmer occurrences... 1493s -reading Kmer occurrences... 1493s 1493s done parsing 100964 Kmers, 100964 added, taking 0 seconds. 1493s 1493s done parsing 100964 Kmers, 100964 added, taking 0 seconds. 1493s STATS_GENERATION_TIME: 0 seconds. 1493s CMD finished (0 seconds) 1494s STATS_GENERATION_TIME: 1 seconds. 1494s CMD finished (1 seconds) 1494s CMD: touch left.fa.K25.stats.ok 1494s CMD finished (0 seconds) 1494s CMD: touch right.fa.K25.stats.ok 1494s CMD finished (0 seconds) 1494s -sorting each stats file by read name. 1494s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort 1494s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort 1494s CMD finished (0 seconds) 1494s CMD finished (0 seconds) 1494s CMD: touch left.fa.K25.stats.sort.ok 1494s CMD finished (0 seconds) 1494s CMD: touch right.fa.K25.stats.sort.ok 1494s CMD finished (0 seconds) 1494s -defining normalized reads 1494s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats 1494s -opening left.fa.K25.stats.sort 1494s -opening right.fa.K25.stats.sort 1494s -done opening files. 1494s CMD finished (0 seconds) 1494s CMD: touch pairs.K25.stats.ok 1494s CMD finished (0 seconds) 1494s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200 --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs 1495s 30472 / 30575 = 99.66% reads selected during normalization. 1495s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles. 1495s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1 1495s CMD finished (1 seconds) 1495s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 1495s CMD finished (0 seconds) 1495s -search and capture. 1495s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture. 1495s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz 1495s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture. 1495s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz 1495s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 1495s CMD finished (0 seconds) 1495s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok 1495s CMD finished (0 seconds) 1495s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq 1495s CMD finished (0 seconds) 1495s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq 1495s CMD finished (0 seconds) 1495s -removing tmp dir /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/tmp_normalized_reads 1495s 1495s 1495s Normalization complete. See outputs: 1495s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq 1495s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq 1495s Saturday, November 2, 2024: 18:01:52 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/normalization.ok 1495s Converting input files. (in parallel)Saturday, November 2, 2024: 18:01:52 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -A -R 1 - >> left.fa 1496s Saturday, November 2, 2024: 18:01:52 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa 1496s Saturday, November 2, 2024: 18:01:52 CMD: touch left.fa.ok 1496s Saturday, November 2, 2024: 18:01:52 CMD: touch right.fa.ok 1496s Saturday, November 2, 2024: 18:01:52 CMD: touch left.fa.ok right.fa.ok 1496s Saturday, November 2, 2024: 18:01:52 CMD: cat left.fa right.fa > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 1496s Saturday, November 2, 2024: 18:01:52 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa.ok 1496s WARNING: --no_run_inchworm parameter in effect. Stopping here prior to running inchworm. 1496s 1496s # stop before chrysalis 1496s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU ${CPU} --output trinity_piecemeal --no_run_chrysalis 1496s 1496s 1496s ______ ____ ____ ____ ____ ______ __ __ 1496s | || \ | || \ | || || | | 1496s | || D ) | | | _ | | | | || | | 1496s |_| |_|| / | | | | | | | |_| |_|| ~ | 1496s | | | \ | | | | | | | | | |___, | 1496s | | | . \ | | | | | | | | | | | 1496s |__| |__|\_||____||__|__||____| |__| |____/ 1496s 1496s Trinity-v2.15.1 1496s 1496s 1496s 1496s Left read files: $VAR1 = [ 1496s 'reads.left.fq.gz' 1496s ]; 1496s Right read files: $VAR1 = [ 1496s 'reads.right.fq.gz' 1496s ]; 1496s 1496s 1496s ---------------------------------------------------------------------------------- 1496s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1496s ---------------------------------------------------------------------------------- 1496s 1496s --------------------------------------------------------------- 1496s ------------ In silico Read Normalization --------------------- 1496s -- (Removing Excess Reads Beyond 200 Coverage -- 1496s --------------------------------------------------------------- 1496s 1496s # running normalization on reads: $VAR1 = [ 1496s [ 1496s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz' 1496s ], 1496s [ 1496s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz' 1496s ] 1496s ]; 1496s 1496s 1496s ------------------------------------------- 1496s ----------- Jellyfish -------------------- 1496s -- (building a k-mer (25) catalog from reads) -- 1496s ------------------------------------------- 1496s 1496s * [Sat Nov 2 18:01:52 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 1498s * [Sat Nov 2 18:01:54 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 1498s * [Sat Nov 2 18:01:54 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 1498s ---------------------------------------------- 1498s --------------- Inchworm (K=25, asm) --------------------- 1498s -- (Linear contig construction from k-mers) -- 1498s ---------------------------------------------- 1498s 1498s * [Sat Nov 2 18:01:54 2024] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --DS --num_threads 2 --PARALLEL_IWORM --min_any_entropy 1.0 -L 25 --no_prune_error_kmers > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa.tmp 1498s Kmer length set to: 25 1498s Min assembly length set to: 25 1498s Monitor turned on, set to: 1 1498s double stranded mode set 1498s min entropy set to: 1 1498s setting number of threads to: 2 1498s -setting parallel iworm mode. 1498s -reading Kmer occurrences... 1498s [0M] Kmers parsed. [0M] Kmers parsed. 1498s done parsing 517949 Kmers, 517949 added, taking 0 seconds. 1498s 1498s TIMING KMER_DB_BUILDING 0 s. 1498s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 1499s Pruned 4114 kmers from catalog. 1499s Pruning time: 1 seconds = 0.0166667 minutes. 1499s 1499s TIMING PRUNING 1 s. 1499s -populating the kmer seed candidate list. 1499s Kcounter hash size: 517949 1499s Processed 513835 non-zero abundance kmers in kcounter. 1499s -Not sorting list of kmers, given parallel mode in effect. 1499s -beginning inchworm contig assembly. 1499s Total kcounter hash size: 517949 vs. sorted list size: 513835 1499s num threads set to: 2 1499s Done opening file. tmp.iworm.fa.pid_84941.thread_0 1499s Done opening file. tmp.iworm.fa.pid_84941.thread_1 1499s 1499s Iworm contig assembly time: 0 seconds = 0 minutes. 1499s 1499s TIMING CONTIG_BUILDING 0 s. 1499s 1499s TIMING PROG_RUNTIME 1 s. 1499s * [Sat Nov 2 18:01:56 2024] Running CMD: mv /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa.tmp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa 1499s Saturday, November 2, 2024: 18:01:56 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa.finished 1500s 1500s 1500s 1500s ######################################################################### 1500s Inchworm is complete. --no_run_chrysalis was specified, so stopping here. 1500s ######################################################################### 1500s 1500s 1500s 1500s # stop before phase 2 1500s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU ${CPU} --output trinity_piecemeal --no_distributed_trinity_exec 1500s 1500s 1500s ______ ____ ____ ____ ____ ______ __ __ 1500s | || \ | || \ | || || | | 1500s | || D ) | | | _ | | | | || | | 1500s |_| |_|| / | | | | | | | |_| |_|| ~ | 1500s | | | \ | | | | | | | | | |___, | 1500s | | | . \ | | | | | | | | | | | 1500s |__| |__|\_||____||__|__||____| |__| |____/ 1500s 1500s Trinity-v2.15.1 1500s 1500s 1500s 1500s Left read files: $VAR1 = [ 1500s 'reads.left.fq.gz' 1500s ]; 1500s Right read files: $VAR1 = [ 1500s 'reads.right.fq.gz' 1500s ]; 1500s 1500s 1500s ---------------------------------------------------------------------------------- 1500s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1500s ---------------------------------------------------------------------------------- 1500s 1500s --------------------------------------------------------------- 1500s ------------ In silico Read Normalization --------------------- 1500s -- (Removing Excess Reads Beyond 200 Coverage -- 1500s --------------------------------------------------------------- 1500s 1500s # running normalization on reads: $VAR1 = [ 1500s [ 1500s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz' 1500s ], 1500s [ 1500s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz' 1500s ] 1500s ]; 1500s 1500s 1500s -------------------------------------------------------- 1500s -------------------- Chrysalis ------------------------- 1500s -- (Contig Clustering & de Bruijn Graph Construction) -- 1500s -------------------------------------------------------- 1500s 1500s inchworm_target: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 1500s bowtie_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 1500s chrysalis_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 1500s 1500s 1500s ####################################################################### 1500s Inchworm file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa detected. 1500s Skipping Inchworm Step, Using Previous Inchworm Assembly 1500s ####################################################################### 1500s 1500s * [Sat Nov 2 18:01:56 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa 100 10 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 1500s * [Sat Nov 2 18:01:56 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 1>/dev/null 1500s * [Sat Nov 2 18:01:56 2024] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa | samtools view -@ 2 -F4 -Sb - | samtools sort -m 536870912 -@ 2 -no /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam" 1504s * [Sat Nov 2 18:02:00 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt 1505s * [Sat Nov 2 18:02:01 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48 -scaffolding /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt 1508s * [Sat Nov 2 18:02:04 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k9,9gr /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted 1508s * [Sat Nov 2 18:02:04 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 1508s * [Sat Nov 2 18:02:04 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 -weld_graph /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out 1508s * [Sat Nov 2 18:02:04 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -min 200 1508s * [Sat Nov 2 18:02:04 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa -f /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -p 10 1512s * [Sat Nov 2 18:02:08 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.sort 1513s Saturday, November 2, 2024: 18:02:09 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/read_partitions/Fb_0/CBin_0 1513s Saturday, November 2, 2024: 18:02:09 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/partitioned_reads.files.list.ok 1513s Saturday, November 2, 2024: 18:02:09 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --full_cleanup --no_distributed_trinity_exec --no_salmon > recursive_trinity.cmds 1513s Saturday, November 2, 2024: 18:02:09 CMD: touch recursive_trinity.cmds.ok 1513s Saturday, November 2, 2024: 18:02:09 CMD: touch recursive_trinity.cmds.ok 1513s 1513s 1513s ################################################################### 1513s ## Stopping here due to --no_distributed_trinity_exec in effect ## 1513s ################################################################### 1513s 1513s 1513s # finish it up 1513s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU ${CPU} --output trinity_piecemeal 1513s 1513s 1513s ______ ____ ____ ____ ____ ______ __ __ 1513s | || \ | || \ | || || | | 1513s | || D ) | | | _ | | | | || | | 1513s |_| |_|| / | | | | | | | |_| |_|| ~ | 1513s | | | \ | | | | | | | | | |___, | 1513s | | | . \ | | | | | | | | | | | 1513s |__| |__|\_||____||__|__||____| |__| |____/ 1513s 1513s Trinity-v2.15.1 1513s 1513s 1513s 1513s Left read files: $VAR1 = [ 1513s 'reads.left.fq.gz' 1513s ]; 1513s Right read files: $VAR1 = [ 1513s 'reads.right.fq.gz' 1513s ]; 1513s 1513s 1513s ---------------------------------------------------------------------------------- 1513s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1513s ---------------------------------------------------------------------------------- 1513s 1513s --------------------------------------------------------------- 1513s ------------ In silico Read Normalization --------------------- 1513s -- (Removing Excess Reads Beyond 200 Coverage -- 1513s --------------------------------------------------------------- 1513s 1513s # running normalization on reads: $VAR1 = [ 1513s [ 1513s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz' 1513s ], 1513s [ 1513s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz' 1513s ] 1513s ]; 1513s 1513s 1513s -------------------------------------------------------- 1513s -------------------- Chrysalis ------------------------- 1513s -- (Contig Clustering & de Bruijn Graph Construction) -- 1513s -------------------------------------------------------- 1513s 1513s inchworm_target: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 1513s bowtie_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 1513s chrysalis_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 1513s 1513s 1513s ####################################################################### 1513s Inchworm file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa detected. 1513s Skipping Inchworm Step, Using Previous Inchworm Assembly 1513s ####################################################################### 1513s 1513s -- Skipping CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa 100 10 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100, checkpoint [/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100.ok] exists. 1513s -- Skipping CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 1>/dev/null, checkpoint [/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100.bowtie2-build.ok] exists. 1513s -- Skipping CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa | samtools view -@ 2 -F4 -Sb - | samtools sort -m 536870912 -@ 2 -no /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam" , checkpoint [/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam.ok] exists. 1513s -- Skipping CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt, checkpoint [/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt.ok] exists. 1513s -- Skipping CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48 -scaffolding /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt, checkpoint [/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.ok] exists. 1513s -- Skipping CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k9,9gr /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted, checkpoint [/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.ok] exists. 1513s -- Skipping CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames, checkpoint [/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames.ok] exists. 1513s -- Skipping CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 -weld_graph /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out, checkpoint [/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out.ok] exists. 1513s -- Skipping CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -min 200, checkpoint [/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta.ok] exists. 1513s -- Skipping CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa -f /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -p 10 , checkpoint [/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.ok] exists. 1513s -- Skipping CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.sort, checkpoint [/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.sort.ok] exists. 1513s 1513s 1513s -------------------------------------------------------------------------------- 1513s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 1513s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 1513s -------------------------------------------------------------------------------- 1513s 1513s Saturday, November 2, 2024: 18:02:09 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 1513s Number of Commands: 39 1598s succeeded(1) 2.5641% completed. succeeded(2) 5.12821% completed. succeeded(3) 7.69231% completed. succeeded(4) 10.2564% completed. succeeded(5) 12.8205% completed. succeeded(6) 15.3846% completed. succeeded(7) 17.9487% completed. succeeded(8) 20.5128% completed. succeeded(9) 23.0769% completed. succeeded(10) 25.641% completed. succeeded(11) 28.2051% completed. succeeded(12) 30.7692% completed. succeeded(13) 33.3333% completed. succeeded(14) 35.8974% completed. succeeded(15) 38.4615% completed. succeeded(16) 41.0256% completed. succeeded(17) 43.5897% completed. succeeded(18) 46.1538% completed. succeeded(19) 48.7179% completed. succeeded(20) 51.2821% completed. succeeded(21) 53.8462% completed. succeeded(22) 56.4103% completed. succeeded(23) 58.9744% completed. succeeded(24) 61.5385% completed. succeeded(25) 64.1026% completed. succeeded(26) 66.6667% completed. succeeded(27) 69.2308% completed. succeeded(28) 71.7949% completed. succeeded(29) 74.359% completed. succeeded(30) 76.9231% completed. succeeded(31) 79.4872% completed. succeeded(32) 82.0513% completed. succeeded(33) 84.6154% completed. succeeded(34) 87.1795% completed. succeeded(35) 89.7436% completed. succeeded(36) 92.3077% completed. succeeded(37) 94.8718% completed. succeeded(38) 97.4359% completed. succeeded(39) 100% completed. 1598s 1598s All commands completed successfully. :-) 1598s 1598s 1598s 1598s ** Harvesting all assembled transcripts into a single multi-fasta file... 1598s 1598s Saturday, November 2, 2024: 18:03:34 CMD: find /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/read_partitions/ -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/Trinity.tmp 1598s * [Sat Nov 2 18:03:34 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 2 1600s * [Sat Nov 2 18:03:36 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta 1600s Saturday, November 2, 2024: 18:03:36 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta.gene_trans_map 1600s 1600s 1600s ############################################################################# 1600s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta 1600s ############################################################################# 1600s 1600s 1600s 1600s 1600s 1600s 1600s ##### Done Running Trinity ##### 1600s 1600s exit 0 1600s ./misc_run_tests/__run_PE_samples_file.min_kmer_cov_3.sh 1600s #!/bin/bash -ve 1600s 1600s ${TRINITY_HOME}/Trinity --samples_file samples.PE.txt \ 1600s --seqType fq \ 1600s --max_memory 1G \ 1600s --min_kmer_cov 3 \ 1600s --output trinity_test_samples_PE_min_kmer_cov_3 1600s 1600s 1600s ______ ____ ____ ____ ____ ______ __ __ 1600s | || \ | || \ | || || | | 1600s | || D ) | | | _ | | | | || | | 1600s |_| |_|| / | | | | | | | |_| |_|| ~ | 1600s | | | \ | | | | | | | | | |___, | 1600s | | | . \ | | | | | | | | | | | 1600s |__| |__|\_||____||__|__||____| |__| |____/ 1600s 1600s Trinity-v2.15.1 1600s 1600s 1600s 1600s Left read files: $VAR1 = [ 1600s 'reads.left.fq.gz', 1600s 'reads2.left.fq.gz' 1600s ]; 1600s Right read files: $VAR1 = [ 1600s 'reads.right.fq.gz', 1600s 'reads2.right.fq.gz' 1600s ]; 1600s Saturday, November 2, 2024: 18:03:36 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3 1600s Saturday, November 2, 2024: 18:03:36 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis 1600s 1600s 1600s ---------------------------------------------------------------------------------- 1600s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1600s ---------------------------------------------------------------------------------- 1600s 1600s --------------------------------------------------------------- 1600s ------------ In silico Read Normalization --------------------- 1600s -- (Removing Excess Reads Beyond 200 Coverage -- 1600s --------------------------------------------------------------- 1600s 1600s # running normalization on reads: $VAR1 = [ 1600s [ 1600s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz', 1600s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz' 1600s ], 1600s [ 1600s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz', 1600s '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz' 1600s ] 1600s ]; 1600s 1600s 1600s Saturday, November 2, 2024: 18:03:36 CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G --max_cov 200 --min_cov 3 --CPU 2 --output /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization --max_CV 10000 --left /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz --right /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz,/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz --pairs_together --PARALLEL_STATS 1600s -prepping seqs 1600s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa 1600s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa 1600s CMD finished (0 seconds) 1600s CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz) >> left.fa 1600s CMD finished (0 seconds) 1600s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz) >> right.fa 1600s CMD finished (0 seconds) 1600s CMD finished (0 seconds) 1600s CMD: touch left.fa.ok 1600s CMD finished (0 seconds) 1600s CMD: touch right.fa.ok 1600s CMD finished (0 seconds) 1600s Done converting input files.CMD: cat left.fa right.fa > both.fa 1600s CMD finished (0 seconds) 1600s CMD: touch both.fa.ok 1600s CMD finished (0 seconds) 1600s -kmer counting. 1600s ------------------------------------------- 1600s ----------- Jellyfish -------------------- 1600s -- (building a k-mer catalog from reads) -- 1600s ------------------------------------------- 1600s 1600s CMD: jellyfish count -t 2 -m 25 -s 100000000 --canonical both.fa 1602s CMD finished (2 seconds) 1602s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 1602s CMD finished (0 seconds) 1602s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 1603s CMD finished (1 seconds) 1603s CMD: touch jellyfish.K25.min2.kmers.fa.success 1603s CMD finished (0 seconds) 1603s -generating stats files 1603s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 --DS > left.fa.K25.stats 1603s -reading Kmer occurrences... 1603s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 --DS > right.fa.K25.stats 1603s -reading Kmer occurrences... 1603s 1603s done parsing 518514 Kmers, 518514 added, taking 0 seconds. 1603s 1603s done parsing 518514 Kmers, 518514 added, taking 0 seconds. 1605s STATS_GENERATION_TIME: 2 seconds. 1605s STATS_GENERATION_TIME: 2 seconds. 1605s CMD finished (2 seconds) 1605s CMD finished (2 seconds) 1605s CMD: touch left.fa.K25.stats.ok 1605s CMD finished (0 seconds) 1605s CMD: touch right.fa.K25.stats.ok 1605s CMD finished (0 seconds) 1605s -sorting each stats file by read name. 1605s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> left.fa.K25.stats.sort 1605s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 1G >> right.fa.K25.stats.sort 1605s CMD finished (0 seconds) 1605s CMD finished (0 seconds) 1605s CMD: touch left.fa.K25.stats.sort.ok 1605s CMD finished (0 seconds) 1605s CMD: touch right.fa.K25.stats.sort.ok 1605s CMD finished (0 seconds) 1605s -defining normalized reads 1605s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats 1605s -opening left.fa.K25.stats.sort 1605s -opening right.fa.K25.stats.sort 1605s -done opening files. 1607s CMD finished (2 seconds) 1607s CMD: touch pairs.K25.stats.ok 1607s CMD finished (0 seconds) 1607s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200 --min_cov 3 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs 1607s 53574 / 61150 = 87.61% reads selected during normalization. 1607s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles. 1607s 2974 / 61150 = 4.86% reads discarded as below minimum coverage threshold=3 1607s CMD finished (0 seconds) 1607s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok 1607s CMD finished (0 seconds) 1607s -search and capture. 1608s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz ... done prepping, now search and capture. 1608s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz 1608s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz ... done prepping, now search and capture. 1608s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz 1608s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz 1608s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz 1609s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC200_minC3_maxCV10000.fq.ok 1609s CMD finished (0 seconds) 1609s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/reads.right.fq.gz_ext_all_reads.normalized_K25_maxC200_minC3_maxCV10000.fq.ok 1609s CMD finished (0 seconds) 1609s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC200_minC3_maxCV10000.fq left.norm.fq 1609s CMD finished (0 seconds) 1609s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/reads.right.fq.gz_ext_all_reads.normalized_K25_maxC200_minC3_maxCV10000.fq right.norm.fq 1609s CMD finished (0 seconds) 1609s -removing tmp dir /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/tmp_normalized_reads 1609s 1609s 1609s Normalization complete. See outputs: 1609s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC200_minC3_maxCV10000.fq 1609s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/reads.right.fq.gz_ext_all_reads.normalized_K25_maxC200_minC3_maxCV10000.fq 1609s Saturday, November 2, 2024: 18:03:45 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/normalization.ok 1609s Converting input files. (in parallel)Saturday, November 2, 2024: 18:03:45 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -A -R 1 - >> left.fa 1609s Saturday, November 2, 2024: 18:03:45 CMD: cat /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa 1609s Saturday, November 2, 2024: 18:03:45 CMD: touch right.fa.ok 1609s Saturday, November 2, 2024: 18:03:45 CMD: touch left.fa.ok 1609s Saturday, November 2, 2024: 18:03:45 CMD: touch left.fa.ok right.fa.ok 1609s Saturday, November 2, 2024: 18:03:45 CMD: cat left.fa right.fa > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa 1609s Saturday, November 2, 2024: 18:03:45 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa.ok 1609s ------------------------------------------- 1609s ----------- Jellyfish -------------------- 1609s -- (building a k-mer (25) catalog from reads) -- 1609s ------------------------------------------- 1609s 1609s * [Sat Nov 2 18:03:45 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa 1611s * [Sat Nov 2 18:03:47 2024] Running CMD: jellyfish dump -L 3 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa 1611s * [Sat Nov 2 18:03:47 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf 1612s ---------------------------------------------- 1612s --------------- Inchworm (K=25, asm) --------------------- 1612s -- (Linear contig construction from k-mers) -- 1612s ---------------------------------------------- 1612s 1612s * [Sat Nov 2 18:03:48 2024] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1 --DS --num_threads 2 --PARALLEL_IWORM --min_any_entropy 1.0 -L 25 --no_prune_error_kmers > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa.tmp 1612s Kmer length set to: 25 1612s Min assembly length set to: 25 1612s Monitor turned on, set to: 1 1612s double stranded mode set 1612s min entropy set to: 1 1612s setting number of threads to: 2 1612s -setting parallel iworm mode. 1612s -reading Kmer occurrences... 1612s 1612s done parsing 96295 Kmers, 96295 added, taking 0 seconds. 1612s 1612s TIMING KMER_DB_BUILDING 0 s. 1612s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005) 1612s Pruned 474 kmers from catalog. 1612s Pruning time: 0 seconds = 0 minutes. 1612s 1612s TIMING PRUNING 0 s. 1612s -populating the kmer seed candidate list. 1612s Kcounter hash size: 96295 1612s Processed 95821 non-zero abundance kmers in kcounter. 1612s -Not sorting list of kmers, given parallel mode in effect. 1612s -beginning inchworm contig assembly. 1612s Total kcounter hash size: 96295 vs. sorted list size: 95821 1612s num threads set to: 2 1612s Done opening file. tmp.iworm.fa.pid_91991.thread_0 1612s Done opening file. tmp.iworm.fa.pid_91991.thread_1 1612s 1612s Iworm contig assembly time: 0 seconds = 0 minutes. 1612s 1612s TIMING CONTIG_BUILDING 0 s. 1612s 1612s TIMING PROG_RUNTIME 0 s. 1612s * [Sat Nov 2 18:03:48 2024] Running CMD: mv /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa.tmp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa 1612s Saturday, November 2, 2024: 18:03:48 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa.finished 1612s -------------------------------------------------------- 1612s -------------------- Chrysalis ------------------------- 1612s -- (Contig Clustering & de Bruijn Graph Construction) -- 1612s -------------------------------------------------------- 1612s 1612s inchworm_target: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa 1612s bowtie_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa 1612s chrysalis_reads_fa: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa 1612s * [Sat Nov 2 18:03:48 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa 100 10 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 1612s * [Sat Nov 2 18:03:48 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 1>/dev/null 1613s * [Sat Nov 2 18:03:49 2024] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa | samtools view -@ 2 -F4 -Sb - | samtools sort -m 268435456 -@ 2 -no /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm.bowtie.nameSorted.bam" 1621s * [Sat Nov 2 18:03:57 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_scaffolds.txt 1622s * [Sat Nov 2 18:03:58 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48 -scaffolding /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_scaffolds.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt 1625s * [Sat Nov 2 18:04:01 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k9,9gr /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt.sorted 1625s * [Sat Nov 2 18:04:01 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames 1625s * [Sat Nov 2 18:04:01 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 -weld_graph /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/GraphFromIwormFasta.out 1625s * [Sat Nov 2 18:04:01 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/bundled_iworm_contigs.fasta -min 200 1625s * [Sat Nov 2 18:04:01 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa -f /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000 -p 10 1633s * [Sat Nov 2 18:04:09 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/readsToComponents.out > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/readsToComponents.out.sort 1633s Saturday, November 2, 2024: 18:04:09 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/read_partitions/Fb_0/CBin_0 1633s Saturday, November 2, 2024: 18:04:09 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/partitioned_reads.files.list.ok 1633s Saturday, November 2, 2024: 18:04:09 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/partitioned_reads.files.list --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --full_cleanup --min_kmer_cov 3 --no_salmon > recursive_trinity.cmds 1633s Saturday, November 2, 2024: 18:04:09 CMD: touch recursive_trinity.cmds.ok 1633s Saturday, November 2, 2024: 18:04:09 CMD: touch recursive_trinity.cmds.ok 1633s 1633s 1633s -------------------------------------------------------------------------------- 1633s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 1633s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 1633s -------------------------------------------------------------------------------- 1633s 1633s Saturday, November 2, 2024: 18:04:09 CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 1633s Number of Commands: 17 1713s succeeded(1) 5.88235% completed. succeeded(2) 11.7647% completed. succeeded(3) 17.6471% completed. succeeded(4) 23.5294% completed. succeeded(5) 29.4118% completed. succeeded(6) 35.2941% completed. succeeded(7) 41.1765% completed. succeeded(8) 47.0588% completed. succeeded(9) 52.9412% completed. succeeded(10) 58.8235% completed. succeeded(11) 64.7059% completed. succeeded(12) 70.5882% completed. succeeded(13) 76.4706% completed. succeeded(14) 82.3529% completed. succeeded(15) 88.2353% completed. succeeded(16) 94.1176% completed. succeeded(17) 100% completed. 1713s 1713s All commands completed successfully. :-) 1713s 1713s 1713s 1713s ** Harvesting all assembled transcripts into a single multi-fasta file... 1713s 1713s Saturday, November 2, 2024: 18:05:29 CMD: find /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/read_partitions/ -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/Trinity.tmp 1713s * [Sat Nov 2 18:05:29 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa 2 1714s * [Sat Nov 2 18:05:30 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta 1714s Saturday, November 2, 2024: 18:05:30 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta.gene_trans_map 1714s 1714s 1714s ############################################################################# 1714s Finished. Final Trinity assemblies are written to /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta 1714s ############################################################################# 1714s 1714s 1714s touch test_all 1714s 1714s 1714s exit 0 1714s make[1]: Leaving directory '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly' 1714s Running example in test_GenomeGuidedTrinity... 1714s make[1]: Entering directory '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity' 1714s ./run_genome-guided_Trinity_use_existing_bam.sh 1714s #!/bin/bash -ve 1714s 1714s if [ -e top100k.Left.fq.gz ] && ! [ -e top100k.Left.fq ] 1714s then 1714s gunzip -c top100k.Left.fq.gz > top100k.Left.fq 1714s fi 1715s 1715s if [ -e top100k.Right.fq.gz ] && ! [ -e top100k.Right.fq ] 1715s then 1715s gunzip -c top100k.Right.fq.gz > top100k.Right.fq 1715s fi 1715s 1715s 1715s 1715s if [ -e top100k.genome.gz ] && ! [ -e top100k.genome ] 1715s then 1715s gunzip -c top100k.genome.gz > top100k.genome 1715s fi 1715s 1715s 1715s 1715s $TRINITY_HOME/Trinity --genome_guided_max_intron 1000 --genome_guided_bam SP2.chr.bam --max_memory 2G --output test_GG_use_bam_trinity_outdir 1715s 1715s 1715s ______ ____ ____ ____ ____ ______ __ __ 1715s | || \ | || \ | || || | | 1715s | || D ) | | | _ | | | | || | | 1715s |_| |_|| / | | | | | | | |_| |_|| ~ | 1715s | | | \ | | | | | | | | | |___, | 1715s | | | . \ | | | | | | | | | | | 1715s |__| |__|\_||____||__|__||____| |__| |____/ 1715s 1715s Trinity-v2.15.1 1715s 1715s 1715s 1715s Saturday, November 2, 2024: 18:05:31 CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl SP2.chr.bam 1716s -appears to be a coordinate sorted bam file. ok. 1716s Saturday, November 2, 2024: 18:05:32 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir 1716s 1716s 1716s ---------------------------------------------------------------------------------- 1716s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1716s ---------------------------------------------------------------------------------- 1716s 1716s -found paired-end aligned read. Running in paired-end mode. 1716s Saturday, November 2, 2024: 18:05:32 CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/SP2.chr.bam.norm_200.bam --keep_secondary /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/SP2.chr.bam 1716s Saturday, November 2, 2024: 18:05:32 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/SP2.chr.bam.norm_200.bam.ok 1716s Saturday, November 2, 2024: 18:05:32 CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/SP2.chr.bam.norm_200.bam -I 1000 --sort_buffer 2G --CPU 2 1716s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --CPU 2 --sort_buffer 2G --sam SP2.chr.bam.norm_200.bam --min_insert_size 1 --max_insert_size 1000 1716s -extracting read coordinates from SP2.chr.bam.norm_200.bam into SP2.chr.bam.norm_200.bam.read_coords 1716s 1718s CMD: touch SP2.chr.bam.norm_200.bam.read_coords.ok 1718s CMD: /usr/bin/sort --parallel=2 -S2G -T . -k1,1 -k2,2 -k4,4n SP2.chr.bam.norm_200.bam.read_coords > SP2.chr.bam.norm_200.bam.read_coords.sort_by_readname 1718s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/SP2.chr.bam.norm_200.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/SP2.chr.bam.norm_200.bam.read_coords.sort_by_readname 1718s CMD: /usr/bin/sort --parallel=2 -S2G -T . -k1,1 -k3,3n SP2.chr.bam.norm_200.bam.frag_coords > SP2.chr.bam.norm_200.bam.frag_coords.coord_sorted 1718s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl SP2.chr.bam.norm_200.bam.frag_coords > SP2.chr.bam.norm_200.bam.frag_coverage.wig 1719s [1000 lines read] scaff:7000000090838467 lend:6192 rend:6455 [2000 lines read] scaff:7000000090838467 lend:7884 rend:8105 [3000 lines read] scaff:7000000090838467 lend:8425 rend:8630 [4000 lines read] scaff:7000000090838467 lend:15701 rend:15766 [5000 lines read] scaff:7000000090838467 lend:28756 rend:28823 [6000 lines read] scaff:7000000090838467 lend:29930 rend:29996 [7000 lines read] scaff:7000000090838467 lend:41235 rend:41435 [8000 lines read] scaff:7000000090838467 lend:48174 rend:48296 [9000 lines read] scaff:7000000090838467 lend:53158 rend:53531 [10000 lines read] scaff:7000000090838467 lend:56567 rend:56797 [11000 lines read] scaff:7000000090838467 lend:57552 rend:57733 [12000 lines read] scaff:7000000090838467 lend:59947 rend:60266 [13000 lines read] scaff:7000000090838467 lend:60447 rend:60807 [14000 lines read] scaff:7000000090838467 lend:64892 rend:65152 [15000 lines read] scaff:7000000090838467 lend:65475 rend:65843 [16000 lines read] scaff:7000000090838467 lend:65983 rend:66211 [17000 lines read] scaff:7000000090838467 lend:66810 rend:67149 [18000 lines read] scaff:7000000090838467 lend:67928 rend:68077 [19000 lines read] scaff:7000000090838467 lend:68811 rend:69080 [20000 lines read] scaff:7000000090838467 lend:74885 rend:75229 [21000 lines read] scaff:7000000090838467 lend:83034 rend:83388 [22000 lines read] scaff:7000000090838467 lend:83791 rend:83830 [23000 lines read] scaff:7000000090838467 lend:84357 rend:84586 [24000 lines read] scaff:7000000090838467 lend:93383 rend:93626 CMD: touch SP2.chr.bam.norm_200.bam.frag_coverage.wig.ok 1719s CMD: /usr/lib/trinityrnaseq/util/support_scripts/define_coverage_partitions.pl SP2.chr.bam.norm_200.bam.frag_coverage.wig 1 + > SP2.chr.bam.norm_200.bam.minC1.gff 1719s CMD: touch SP2.chr.bam.norm_200.bam.minC1.gff.ok 1719s CMD: /usr/lib/trinityrnaseq/util/support_scripts/extract_reads_per_partition.pl --partitions_gff SP2.chr.bam.norm_200.bam.minC1.gff --coord_sorted_SAM SP2.chr.bam.norm_200.bam --parts_per_directory 100 --min_reads_per_partition 10 1719s // parsing paritions. 1719s [71] -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/14_122.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/212_1291.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/1392_1648.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/1797_2125.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/2163_3611.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/3633_3710.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/4913_5681.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/9938_10435.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/11319_11903.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/12073_12996.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/13623_13950.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/14321_14565.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/15124_16713.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/16949_17135.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17151_17239.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17291_17395.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17403_17460.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17486_18615.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/18669_19255.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/19312_19749.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/19806_20057.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/25542_25904.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/27107_27961.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads 1719s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/29764_32484.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/33570_35223.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/35276_35333.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/35616_35657.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/35667_36204.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/40913_41816.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/42003_43278.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/43414_43636.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/45059_45550.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/45591_49924.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/50916_53857.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/54299_54404.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/56263_56322.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/56460_59191.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/59428_61023.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/64539_69762.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/71026_71306.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/71566_71786.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/72348_72436.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/73883_73950.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/76379_76542.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/77783_78299.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/79543_79626.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/80570_80778.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/81974_82231.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/85575_85999.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads 1720s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/90691_93939.trinity.reads 1721s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/95200_96973.trinity.reads 1721s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/98644_98711.trinity.reads 1721s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads 1721s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/99132_100027.trinity.reads 1721s CMD: touch Dir_SP2.chr.bam.norm_200.bam.minC1.gff.ok 1721s ## 1721s Done 1721s ## 1721s 1721s Saturday, November 2, 2024: 18:05:37 CMD: touch partitions.ok 1721s Saturday, November 2, 2024: 18:05:37 CMD: find Dir_* -name '*reads' > read_files.list 1721s Saturday, November 2, 2024: 18:05:37 CMD: touch read_files.list.ok 1721s Saturday, November 2, 2024: 18:05:37 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file read_files.list --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --full_cleanup > trinity_GG.cmds 1721s Saturday, November 2, 2024: 18:05:37 CMD: touch trinity_GG.cmds.ok 1721s Saturday, November 2, 2024: 18:05:37 CMD: touch trinity_GG.cmds.ok 1721s 1721s 1721s -------------------------------------------------------------------------------- 1721s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 1721s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 1721s -------------------------------------------------------------------------------- 1721s 1721s Saturday, November 2, 2024: 18:05:37 CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -v -shuffle 1721s Number of Commands: 37 1794s succeeded(1) 2.7027% completed. succeeded(2) 5.40541% completed. succeeded(3) 8.10811% completed. succeeded(4) 10.8108% completed. succeeded(5) 13.5135% completed. succeeded(6) 16.2162% completed. succeeded(7) 18.9189% completed. succeeded(8) 21.6216% completed. succeeded(9) 24.3243% completed. succeeded(10) 27.027% completed. succeeded(11) 29.7297% completed. succeeded(12) 32.4324% completed. succeeded(13) 35.1351% completed. succeeded(14) 37.8378% completed. succeeded(15) 40.5405% completed. succeeded(16) 43.2432% completed. succeeded(17) 45.9459% completed. succeeded(18) 48.6487% completed. succeeded(19) 51.3513% completed. succeeded(20) 54.0541% completed. succeeded(21) 56.7568% completed. succeeded(22) 59.4595% completed. succeeded(23) 62.1622% completed. succeeded(24) 64.8649% completed. succeeded(25) 67.5676% completed. succeeded(26) 70.2703% completed. succeeded(27) 72.973% completed. succeeded(28) 75.6757% completed. succeeded(29) 78.3784% completed. succeeded(30) 81.0811% completed. succeeded(31) 83.7838% completed. succeeded(32) 86.4865% completed. succeeded(33) 89.1892% completed. succeeded(34) 91.8919% completed. succeeded(35) 94.5946% completed. succeeded(36) 97.2973% completed. succeeded(37) 100% completed. 1794s 1794s All commands completed successfully. :-) 1794s 1794s Saturday, November 2, 2024: 18:06:50 CMD: find Dir_* -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta.tmp 1794s Saturday, November 2, 2024: 18:06:50 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta.gene_trans_map 1794s 1794s 1794s Finished. See /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta for reconstructed transcripts 1794s 1794s 1794s asmsize=$(wc -c <"test_GG_use_bam_trinity_outdir/Trinity-GG.fasta") 1794s if [ $asmsize -le 50000 ]; then 1794s echo "Error, test_GG_use_bam_trinity_outdir/Trinity-GG.fasta potentially incomplete" 1794s exit 1 1794s else 1794s echo "ok" 1794s exit 0 1794s fi 1794s ok 1794s ./run_Schizo_TrinityGG_jaccard_clip.sh 1794s #!/bin/bash -ve 1794s 1794s $TRINITY_HOME/Trinity --genome_guided_bam SP2.chr.bam --max_memory 1G --CPU 2 --genome_guided_max_intron 1000 --jaccard_clip --SS_lib_type RF --output test_Schizo_trinityGG_jaccard_RF_outdir 1794s 1794s 1794s ______ ____ ____ ____ ____ ______ __ __ 1794s | || \ | || \ | || || | | 1794s | || D ) | | | _ | | | | || | | 1794s |_| |_|| / | | | | | | | |_| |_|| ~ | 1794s | | | \ | | | | | | | | | |___, | 1794s | | | . \ | | | | | | | | | | | 1794s |__| |__|\_||____||__|__||____| |__| |____/ 1794s 1794s Trinity-v2.15.1 1794s 1794s 1794s 1794s Saturday, November 2, 2024: 18:06:50 CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl SP2.chr.bam 1794s -appears to be a coordinate sorted bam file. ok. 1794s Saturday, November 2, 2024: 18:06:50 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir 1794s 1794s 1794s ---------------------------------------------------------------------------------- 1794s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1794s ---------------------------------------------------------------------------------- 1794s 1794s -found paired-end aligned read. Running in paired-end mode. 1794s Saturday, November 2, 2024: 18:06:50 CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam --keep_secondary /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/SP2.chr.bam 1795s Saturday, November 2, 2024: 18:06:51 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam.ok 1795s Saturday, November 2, 2024: 18:06:51 CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam -I 1000 --sort_buffer 1G --CPU 2 --SS_lib_type RF 1795s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam RF 1795s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --CPU 2 --sort_buffer 1G --sam SP2.chr.bam.norm_200.bam.+.sam --min_insert_size 1 --max_insert_size 1000 1795s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --CPU 2 --sort_buffer 1G --sam SP2.chr.bam.norm_200.bam.-.sam --min_insert_size 1 --max_insert_size 1000 1796s -extracting read coordinates from SP2.chr.bam.norm_200.bam.+.sam into SP2.chr.bam.norm_200.bam.+.sam.read_coords 1796s 1796s -extracting read coordinates from SP2.chr.bam.norm_200.bam.-.sam into SP2.chr.bam.norm_200.bam.-.sam.read_coords 1796s 1796s CMD: touch SP2.chr.bam.norm_200.bam.-.sam.read_coords.ok 1796s CMD: /usr/bin/sort --parallel=2 -S1G -T . -k1,1 -k2,2 -k4,4n SP2.chr.bam.norm_200.bam.-.sam.read_coords > SP2.chr.bam.norm_200.bam.-.sam.read_coords.sort_by_readname 1796s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam.-.sam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam.-.sam.read_coords.sort_by_readname 1796s CMD: /usr/bin/sort --parallel=2 -S1G -T . -k1,1 -k3,3n SP2.chr.bam.norm_200.bam.-.sam.frag_coords > SP2.chr.bam.norm_200.bam.-.sam.frag_coords.coord_sorted 1796s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl SP2.chr.bam.norm_200.bam.-.sam.frag_coords > SP2.chr.bam.norm_200.bam.-.sam.frag_coverage.wig 1796s [1000 lines read] scaff:7000000090838467 lend:6194 rend:6433 [2000 lines read] scaff:7000000090838467 lend:46308 rend:46696 CMD: touch SP2.chr.bam.norm_200.bam.+.sam.read_coords.ok 1796s CMD: /usr/bin/sort --parallel=2 -S1G -T . -k1,1 -k2,2 -k4,4n SP2.chr.bam.norm_200.bam.+.sam.read_coords > SP2.chr.bam.norm_200.bam.+.sam.read_coords.sort_by_readname 1796s [3000 lines read] scaff:7000000090838467 lend:59573 rend:59951 [4000 lines read] scaff:7000000090838467 lend:60068 rend:60313 [5000 lines read] scaff:7000000090838467 lend:60602 rend:60807 CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam.+.sam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam.+.sam.read_coords.sort_by_readname 1796s [6000 lines read] scaff:7000000090838467 lend:65099 rend:65468 [7000 lines read] scaff:7000000090838467 lend:65621 rend:65957 CMD: /usr/bin/sort --parallel=2 -S1G -T . -k1,1 -k3,3n SP2.chr.bam.norm_200.bam.+.sam.frag_coords > SP2.chr.bam.norm_200.bam.+.sam.frag_coords.coord_sorted 1796s [8000 lines read] scaff:7000000090838467 lend:66173 rend:66538 [9000 lines read] scaff:7000000090838467 lend:88962 rend:89278 CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl SP2.chr.bam.norm_200.bam.+.sam.frag_coords > SP2.chr.bam.norm_200.bam.+.sam.frag_coverage.wig 1796s CMD: touch SP2.chr.bam.norm_200.bam.-.sam.frag_coverage.wig.ok 1796s CMD: /usr/lib/trinityrnaseq/util/support_scripts/define_coverage_partitions.pl SP2.chr.bam.norm_200.bam.-.sam.frag_coverage.wig 1 - > SP2.chr.bam.norm_200.bam.-.sam.minC1.gff 1797s [1000 lines read] scaff:7000000090838467 lend:8022 rend:8237 [2000 lines read] scaff:7000000090838467 lend:8568 rend:8635 [3000 lines read] scaff:7000000090838467 lend:21591 rend:21888 [4000 lines read] scaff:7000000090838467 lend:29215 rend:29340 [5000 lines read] scaff:7000000090838467 lend:30519 rend:30759 CMD: touch SP2.chr.bam.norm_200.bam.-.sam.minC1.gff.ok 1797s CMD: /usr/lib/trinityrnaseq/util/support_scripts/extract_reads_per_partition.pl --partitions_gff SP2.chr.bam.norm_200.bam.-.sam.minC1.gff --coord_sorted_SAM SP2.chr.bam.norm_200.bam.-.sam --parts_per_directory 100 --min_reads_per_partition 10 --SS_lib_type RF 1797s [6000 lines read] scaff:7000000090838467 lend:52660 rend:52989 // parsing paritions. 1797s [73] -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/14_122.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/1392_1648.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/1797_2125.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3633_3710.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/4913_5470.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5606_5681.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads 1797s [7000 lines read] scaff:7000000090838467 lend:56475 rend:56834 [8000 lines read] scaff:7000000090838467 lend:57224 rend:57489 -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/7478_7778.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/11319_11575.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/13623_13950.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/16160_16227.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/16322_16713.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/16949_17135.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/18334_18615.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/18745_19255.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/19312_19749.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/19806_20057.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/21538_21869.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/25632_25904.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/28689_28755.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/28953_29020.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads 1797s [9000 lines read] scaff:7000000090838467 lend:67627 rend:67818 -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/35276_35333.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/35667_36050.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/43050_43256.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/43414_43636.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads 1797s [10000 lines read] scaff:7000000090838467 lend:68505 rend:68690 -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/52320_52590.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/52965_53480.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/54299_54404.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55029_55235.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55243_55272.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55367_55660.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55765_56138.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56263_56322.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads 1797s [11000 lines read] scaff:7000000090838467 lend:69245 rend:69544 -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads 1797s [12000 lines read] scaff:7000000090838467 lend:82862 rend:83065 [13000 lines read] scaff:7000000090838467 lend:83622 rend:83842 [14000 lines read] scaff:7000000090838467 lend:84137 rend:84436 -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/63225_63476.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads 1797s CMD: touch SP2.chr.bam.norm_200.bam.+.sam.frag_coverage.wig.ok 1797s CMD: /usr/lib/trinityrnaseq/util/support_scripts/define_coverage_partitions.pl SP2.chr.bam.norm_200.bam.+.sam.frag_coverage.wig 1 + > SP2.chr.bam.norm_200.bam.+.sam.minC1.gff 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/67085_67370.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/69270_69337.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/71566_71786.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/73883_73950.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/76379_76542.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/77783_78299.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80570_80778.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81974_82231.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/83425_83673.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/83688_83987.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/84011_84078.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/85575_85999.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads 1797s CMD: touch SP2.chr.bam.norm_200.bam.+.sam.minC1.gff.ok 1797s CMD: /usr/lib/trinityrnaseq/util/support_scripts/extract_reads_per_partition.pl --partitions_gff SP2.chr.bam.norm_200.bam.+.sam.minC1.gff --coord_sorted_SAM SP2.chr.bam.norm_200.bam.+.sam --parts_per_directory 100 --min_reads_per_partition 10 --SS_lib_type RF 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/98744_98781.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads 1797s CMD: touch Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff.ok 1797s // parsing paritions. 1797s [57] -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/872_939.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/963_1208.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/2378_2430.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/3465_3611.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/3804_3872.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/5374_5664.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/9938_10435.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/11471_11903.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/14321_14565.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/18669_18911.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/25542_25867.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/27107_27395.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/27630_27959.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/31628_31881.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/31893_32259.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/35616_35657.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/35987_36204.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/40913_41123.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/41133_41404.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/45059_45550.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/46429_46482.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/59886_59966.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/60255_61023.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/64782_64821.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/65880_65925.trinity.reads 1797s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads 1798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/71026_71306.trinity.reads 1798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/72348_72436.trinity.reads 1798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads 1798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/79543_79626.trinity.reads 1798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads 1798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/88618_88826.trinity.reads 1798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads 1798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads 1798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98644_98711.trinity.reads 1798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads 1798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99067_99099.trinity.reads 1798s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads 1798s CMD: touch Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff.ok 1798s ## 1798s Done 1798s ## 1798s 1798s Saturday, November 2, 2024: 18:06:54 CMD: touch partitions.ok 1798s Saturday, November 2, 2024: 18:06:54 CMD: find Dir_* -name '*reads' > read_files.list 1798s Saturday, November 2, 2024: 18:06:54 CMD: touch read_files.list.ok 1798s Saturday, November 2, 2024: 18:06:54 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file read_files.list --CPU 1 --max_memory 1G --run_as_paired --SS_lib_type F --seqType fa --trinity_complete --full_cleanup --jaccard_clip > trinity_GG.cmds 1798s Saturday, November 2, 2024: 18:06:54 CMD: touch trinity_GG.cmds.ok 1798s Saturday, November 2, 2024: 18:06:54 CMD: touch trinity_GG.cmds.ok 1798s 1798s 1798s -------------------------------------------------------------------------------- 1798s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 1798s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 1798s -------------------------------------------------------------------------------- 1798s 1798s Saturday, November 2, 2024: 18:06:54 CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -v -shuffle 1798s Number of Commands: 53 1798s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1798s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1798s bt2 index files: $VAR1 = []; 1798s Note - bowtie-build indices do not yet exist. Indexing genome now. 1798s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1798s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1798s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1798s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1798s bt2 index files: $VAR1 = []; 1798s Note - bowtie-build indices do not yet exist. Indexing genome now. 1798s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1799s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1799s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1799s 85 reads; of these: 1799s 85 (100.00%) were unpaired; of these: 1799s 3 (3.53%) aligned 0 times 1799s 82 (96.47%) aligned exactly 1 time 1799s 0 (0.00%) aligned >1 times 1799s 96.47% overall alignment rate 1799s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1799s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1799s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1799s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1799s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1799s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1799s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1799s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1799s 1799s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1799s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1799s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1799s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1799s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1799s -processing jaccard pair sensor 1799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1799s 1717 reads; of these: 1799s 1717 (100.00%) were unpaired; of these: 1799s 1 (0.06%) aligned 0 times 1799s 1511 (88.00%) aligned exactly 1 time 1799s 205 (11.94%) aligned >1 times 1799s 99.94% overall alignment rate 1799s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads.out/inchworm.fa.clipped.fa 1799s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1799s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1799s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1799s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1799s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1799s 1799s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1799s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1799s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1799s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1799s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1799s -processing jaccard pair sensor 1799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1799s [1000 lines read] scaff:a2;50 lend:1 rend:68 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1799s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads.out/inchworm.fa.clipped.fa 1803s succeeded(1) 1.88679% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1803s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1803s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1803s bt2 index files: $VAR1 = []; 1803s Note - bowtie-build indices do not yet exist. Indexing genome now. 1803s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1803s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1803s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1803s 2128 reads; of these: 1803s 2128 (100.00%) were unpaired; of these: 1803s 6 (0.28%) aligned 0 times 1803s 1722 (80.92%) aligned exactly 1 time 1803s 400 (18.80%) aligned >1 times 1803s 99.72% overall alignment rate 1803s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1803s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1804s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1804s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1804s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1804s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1804s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1804s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1804s succeeded(2) 3.77358% completed. -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1804s 1804s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1804s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1804s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1804s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1804s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1804s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1804s -processing jaccard pair sensor 1804s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1804s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1804s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1804s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1804s bt2 index files: $VAR1 = []; 1804s Note - bowtie-build indices do not yet exist. Indexing genome now. 1804s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1804s [1000 lines read] scaff:a1;40 lend:1330 rend:1645 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1804s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads.out/inchworm.fa.clipped.fa 1804s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1804s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1804s 30 reads; of these: 1804s 30 (100.00%) were unpaired; of these: 1804s 0 (0.00%) aligned 0 times 1804s 18 (60.00%) aligned exactly 1 time 1804s 12 (40.00%) aligned >1 times 1804s 100.00% overall alignment rate 1804s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1804s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1804s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1804s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1804s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1805s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1805s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1805s 1805s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1805s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1805s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1805s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1805s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1805s -processing jaccard pair sensor 1805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1805s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads.out/inchworm.fa.clipped.fa 1806s succeeded(3) 5.66038% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1806s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1807s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1807s bt2 index files: $VAR1 = []; 1807s Note - bowtie-build indices do not yet exist. Indexing genome now. 1807s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1807s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1807s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1807s 24 reads; of these: 1807s 24 (100.00%) were unpaired; of these: 1807s 1 (4.17%) aligned 0 times 1807s 23 (95.83%) aligned exactly 1 time 1807s 0 (0.00%) aligned >1 times 1807s 95.83% overall alignment rate 1807s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1807s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1807s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1807s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1807s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1807s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1807s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1807s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1807s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1807s 1807s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1807s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1808s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1808s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1808s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1808s -processing jaccard pair sensor 1808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1808s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads.out/inchworm.fa.clipped.fa 1810s succeeded(4) 7.54717% completed. succeeded(5) 9.43396% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1810s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1810s bt2 index files: $VAR1 = []; 1810s Note - bowtie-build indices do not yet exist. Indexing genome now. 1810s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1810s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1810s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1810s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1810s bt2 index files: $VAR1 = []; 1810s Note - bowtie-build indices do not yet exist. Indexing genome now. 1810s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1810s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1810s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1811s 309 reads; of these: 1811s 309 (100.00%) were unpaired; of these: 1811s 3 (0.97%) aligned 0 times 1811s 201 (65.05%) aligned exactly 1 time 1811s 105 (33.98%) aligned >1 times 1811s 99.03% overall alignment rate 1811s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1811s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1811s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1811s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1811s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1811s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1811s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1811s 213 reads; of these: 1811s 213 (100.00%) were unpaired; of these: 1811s 1 (0.47%) aligned 0 times 1811s 121 (56.81%) aligned exactly 1 time 1811s 91 (42.72%) aligned >1 times 1811s 99.53% overall alignment rate 1811s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1811s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1811s 1811s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1811s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1811s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1811s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1811s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1811s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1811s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1811s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1811s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1811s -processing jaccard pair sensor 1811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1811s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1811s 1811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1811s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1811s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1811s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1811s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads.out/inchworm.fa.clipped.fa 1811s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1811s -processing jaccard pair sensor 1811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1811s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads.out/inchworm.fa.clipped.fa 1814s succeeded(6) 11.3208% completed. succeeded(7) 13.2075% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1814s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1814s bt2 index files: $VAR1 = []; 1814s Note - bowtie-build indices do not yet exist. Indexing genome now. 1814s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1814s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1814s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1814s bt2 index files: $VAR1 = []; 1814s Note - bowtie-build indices do not yet exist. Indexing genome now. 1814s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1814s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1814s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1814s 10 reads; of these: 1814s 10 (100.00%) were unpaired; of these: 1814s 2 (20.00%) aligned 0 times 1814s 8 (80.00%) aligned exactly 1 time 1814s 0 (0.00%) aligned >1 times 1814s 80.00% overall alignment rate 1814s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1814s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1814s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1814s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1814s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1814s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1814s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1814s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1815s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1815s 1815s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1815s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1815s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1815s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1815s 10 reads; of these: 1815s 10 (100.00%) were unpaired; of these: 1815s 7 (70.00%) aligned 0 times 1815s 3 (30.00%) aligned exactly 1 time 1815s 0 (0.00%) aligned >1 times 1815s 30.00% overall alignment rate 1815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1815s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1815s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1815s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1815s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1815s -processing jaccard pair sensor 1815s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1815s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads.out/inchworm.fa.clipped.fa 1815s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1815s 1815s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1815s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1815s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1815s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1815s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1815s -processing jaccard pair sensor 1815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1815s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads.out/inchworm.fa.clipped.fa 1816s succeeded(8) 15.0943% completed. succeeded(9) 16.9811% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1816s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1816s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1816s bt2 index files: $VAR1 = []; 1816s Note - bowtie-build indices do not yet exist. Indexing genome now. 1816s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1816s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1816s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1816s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1816s bt2 index files: $VAR1 = []; 1816s Note - bowtie-build indices do not yet exist. Indexing genome now. 1816s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1817s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1817s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1817s 277 reads; of these: 1817s 277 (100.00%) were unpaired; of these: 1817s 0 (0.00%) aligned 0 times 1817s 277 (100.00%) aligned exactly 1 time 1817s 0 (0.00%) aligned >1 times 1817s 100.00% overall alignment rate 1817s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1817s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1817s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1817s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1817s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1817s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1817s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1817s 30 reads; of these: 1817s 30 (100.00%) were unpaired; of these: 1817s 9 (30.00%) aligned 0 times 1817s 21 (70.00%) aligned exactly 1 time 1817s 0 (0.00%) aligned >1 times 1817s 70.00% overall alignment rate 1817s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1817s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1817s 1817s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1817s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1817s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1817s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1817s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1817s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1817s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1817s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1817s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1817s -processing jaccard pair sensor 1817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1817s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1817s 1817s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1817s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1817s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1817s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads.out/inchworm.fa.clipped.fa 1817s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1817s -processing jaccard pair sensor 1817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1817s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads.out/inchworm.fa.clipped.fa 1819s succeeded(10) 18.8679% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1819s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1819s bt2 index files: $VAR1 = []; 1819s Note - bowtie-build indices do not yet exist. Indexing genome now. 1819s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1819s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1819s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1819s 51 reads; of these: 1819s 51 (100.00%) were unpaired; of these: 1819s 4 (7.84%) aligned 0 times 1819s 47 (92.16%) aligned exactly 1 time 1819s 0 (0.00%) aligned >1 times 1819s 92.16% overall alignment rate 1819s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1819s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1819s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1819s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1819s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1819s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1819s 1819s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1819s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1819s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1819s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1819s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1819s -processing jaccard pair sensor 1819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1819s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads.out/inchworm.fa.clipped.fa 1820s succeeded(11) 20.7547% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1820s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1820s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1820s bt2 index files: $VAR1 = []; 1820s Note - bowtie-build indices do not yet exist. Indexing genome now. 1820s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1820s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1820s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1820s 454 reads; of these: 1820s 454 (100.00%) were unpaired; of these: 1820s 1 (0.22%) aligned 0 times 1820s 368 (81.06%) aligned exactly 1 time 1820s 85 (18.72%) aligned >1 times 1820s 99.78% overall alignment rate 1820s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1820s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1820s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1820s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1820s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1820s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1820s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1820s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1820s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1820s 1820s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1820s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1820s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1820s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1820s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1820s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1820s -processing jaccard pair sensor 1821s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1821s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1821s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads.out/inchworm.fa.clipped.fa 1823s succeeded(12) 22.6415% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1823s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1823s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1823s succeeded(13) 24.5283% completed. bt2 index files: $VAR1 = []; 1823s Note - bowtie-build indices do not yet exist. Indexing genome now. 1823s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1824s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1824s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1824s 2557 reads; of these: 1824s 2557 (100.00%) were unpaired; of these: 1824s 11 (0.43%) aligned 0 times 1824s 1332 (52.09%) aligned exactly 1 time 1824s 1214 (47.48%) aligned >1 times 1824s 99.57% overall alignment rate 1824s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1824s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1824s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1824s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1824s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1824s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1824s 1824s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1824s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1824s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1824s bt2 index files: $VAR1 = []; 1824s Note - bowtie-build indices do not yet exist. Indexing genome now. 1824s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1825s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1825s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1825s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1825s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1825s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1825s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1825s -processing jaccard pair sensor 1825s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1825s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1825s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1825s [1000 lines read] scaff:a1;81 lend:250 rend:502 [2000 lines read] scaff:a22;2 lend:4 rend:34 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1825s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads.out/inchworm.fa.clipped.fa 1826s 7038 reads; of these: 1826s 7038 (100.00%) were unpaired; of these: 1826s 25 (0.36%) aligned 0 times 1826s 2368 (33.65%) aligned exactly 1 time 1826s 4645 (66.00%) aligned >1 times 1826s 99.64% overall alignment rate 1826s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1826s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1826s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1826s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam 1826s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam 1826s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1826s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam 1826s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1826s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1827s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1827s 1827s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1827s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1827s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1827s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1827s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1827s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1827s -processing jaccard pair sensor 1828s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1829s [1000 lines read] scaff:a16;2 lend:11 rend:42 [2000 lines read] scaff:a1;131 lend:621 rend:903 [3000 lines read] scaff:a1;131 lend:1136 rend:1543 [4000 lines read] scaff:a1;131 lend:1699 rend:1900 [5000 lines read] scaff:a25;2 lend:31 rend:73 [6000 lines read] scaff:a30;2 lend:1 rend:37 [7000 lines read] scaff:a3;9 lend:1 rend:43 [8000 lines read] scaff:a53;2 lend:1 rend:49 [9000 lines read] scaff:a5;2 lend:16 rend:60 [10000 lines read] scaff:a69;2 lend:1 rend:43 [11000 lines read] scaff:a79;2 lend:1 rend:50 [12000 lines read] scaff:a9;3 lend:1 rend:36 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1829s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads.out/inchworm.fa.clipped.fa 1830s succeeded(14) 26.4151% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1830s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1830s bt2 index files: $VAR1 = []; 1830s Note - bowtie-build indices do not yet exist. Indexing genome now. 1830s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1830s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1830s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1830s 77 reads; of these: 1830s 77 (100.00%) were unpaired; of these: 1830s 2 (2.60%) aligned 0 times 1830s 75 (97.40%) aligned exactly 1 time 1830s 0 (0.00%) aligned >1 times 1830s 97.40% overall alignment rate 1830s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1830s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1830s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1830s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1830s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1830s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1830s 1830s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1830s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1830s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1830s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1830s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1830s -processing jaccard pair sensor 1830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1830s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads.out/inchworm.fa.clipped.fa 1835s succeeded(15) 28.3019% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1835s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1835s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1835s bt2 index files: $VAR1 = []; 1835s Note - bowtie-build indices do not yet exist. Indexing genome now. 1835s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1835s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1835s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1836s succeeded(16) 30.1887% completed. 5953 reads; of these: 1836s 5953 (100.00%) were unpaired; of these: 1836s 11 (0.18%) aligned 0 times 1836s 3807 (63.95%) aligned exactly 1 time 1836s 2135 (35.86%) aligned >1 times 1836s 99.82% overall alignment rate 1836s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1836s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1836s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1836s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1836s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1836s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1836s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1836s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1836s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1836s 1836s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1836s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1836s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1836s bt2 index files: $VAR1 = []; 1836s Note - bowtie-build indices do not yet exist. Indexing genome now. 1836s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1836s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1836s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1836s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1836s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1837s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1837s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1837s -processing jaccard pair sensor 1837s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1837s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1837s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1837s [1000 lines read] scaff:a1;90 lend:143 rend:454 [2000 lines read] scaff:a1;90 lend:1115 rend:1442 [3000 lines read] scaff:a1;90 lend:1905 rend:2258 [4000 lines read] scaff:a21;2 lend:5 rend:43 [5000 lines read] scaff:a39;2 lend:10 rend:46 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1837s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads.out/inchworm.fa.clipped.fa 1837s 5664 reads; of these: 1837s 5664 (100.00%) were unpaired; of these: 1837s 8 (0.14%) aligned 0 times 1837s 3217 (56.80%) aligned exactly 1 time 1837s 2439 (43.06%) aligned >1 times 1837s 99.86% overall alignment rate 1837s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1837s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1838s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1838s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1838s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1838s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1838s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1838s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1838s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1838s 1838s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1838s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1838s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1839s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1839s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1839s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1839s -processing jaccard pair sensor 1839s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1839s [1000 lines read] scaff:a1;95 lend:117 rend:350 [2000 lines read] scaff:a1;95 lend:928 rend:1277 [3000 lines read] scaff:a1;95 lend:1591 rend:1658 [4000 lines read] scaff:a26;2 lend:1 rend:43 [5000 lines read] scaff:a2;68 lend:175 rend:389 [6000 lines read] scaff:a39;2 lend:1 rend:42 [7000 lines read] scaff:a6;42 lend:15 rend:68 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1839s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads.out/inchworm.fa.clipped.fa 1845s succeeded(17) 32.0755% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1845s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1845s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1845s bt2 index files: $VAR1 = []; 1845s Note - bowtie-build indices do not yet exist. Indexing genome now. 1845s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1846s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1846s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1846s 24 reads; of these: 1846s 24 (100.00%) were unpaired; of these: 1846s 3 (12.50%) aligned 0 times 1846s 21 (87.50%) aligned exactly 1 time 1846s 0 (0.00%) aligned >1 times 1846s 87.50% overall alignment rate 1846s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1846s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1846s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1846s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1846s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1846s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1846s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1846s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1846s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1846s 1846s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1846s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1846s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1846s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1846s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1846s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1846s -processing jaccard pair sensor 1846s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1846s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1846s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads.out/inchworm.fa.clipped.fa 1846s succeeded(18) 33.9623% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1846s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1846s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1846s bt2 index files: $VAR1 = []; 1846s Note - bowtie-build indices do not yet exist. Indexing genome now. 1846s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1846s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1846s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1847s 1733 reads; of these: 1847s 1733 (100.00%) were unpaired; of these: 1847s 0 (0.00%) aligned 0 times 1847s 794 (45.82%) aligned exactly 1 time 1847s 939 (54.18%) aligned >1 times 1847s 100.00% overall alignment rate 1847s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1847s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1847s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1847s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1847s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1847s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1847s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1847s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1847s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1847s 1847s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1847s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1847s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1847s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1847s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1847s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1847s -processing jaccard pair sensor 1847s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1847s [1000 lines read] scaff:a22;2 lend:1 rend:49 succeeded(19) 35.8491% completed. [2000 lines read] scaff:a3;97 lend:65 rend:131 [3000 lines read] scaff:a9;12 lend:1 rend:38 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1847s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads.out/inchworm.fa.clipped.fa 1848s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1848s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1848s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1848s bt2 index files: $VAR1 = []; 1848s Note - bowtie-build indices do not yet exist. Indexing genome now. 1848s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1848s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1848s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1848s 115 reads; of these: 1848s 115 (100.00%) were unpaired; of these: 1848s 6 (5.22%) aligned 0 times 1848s 109 (94.78%) aligned exactly 1 time 1848s 0 (0.00%) aligned >1 times 1848s 94.78% overall alignment rate 1848s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1848s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1848s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1848s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1848s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1848s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1848s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1848s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1848s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1848s 1848s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1848s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1848s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1848s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1848s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1848s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1848s -processing jaccard pair sensor 1848s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1848s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1848s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads.out/inchworm.fa.clipped.fa 1851s succeeded(20) 37.7359% completed. succeeded(21) 39.6226% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1851s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1851s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1851s bt2 index files: $VAR1 = []; 1851s Note - bowtie-build indices do not yet exist. Indexing genome now. 1851s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1851s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1851s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1852s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1852s bt2 index files: $VAR1 = []; 1852s Note - bowtie-build indices do not yet exist. Indexing genome now. 1852s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1852s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1852s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1852s 20 reads; of these: 1852s 20 (100.00%) were unpaired; of these: 1852s 12 (60.00%) aligned 0 times 1852s 8 (40.00%) aligned exactly 1 time 1852s 0 (0.00%) aligned >1 times 1852s 40.00% overall alignment rate 1852s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1852s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1852s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1852s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1852s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1852s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1852s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1852s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1852s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1852s 1852s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1852s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1852s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1852s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1852s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1852s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1852s -processing jaccard pair sensor 1852s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1852s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1852s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1852s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1852s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads.out/inchworm.fa.clipped.fa 1852s 34 reads; of these: 1852s 34 (100.00%) were unpaired; of these: 1852s 1 (2.94%) aligned 0 times 1852s 33 (97.06%) aligned exactly 1 time 1852s 0 (0.00%) aligned >1 times 1852s 97.06% overall alignment rate 1852s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1852s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1852s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1852s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1852s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1852s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1852s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1852s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1852s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1852s 1852s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1852s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1852s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1852s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1852s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1852s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1852s -processing jaccard pair sensor 1852s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1852s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1852s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads.out/inchworm.fa.clipped.fa 1854s succeeded(22) 41.5094% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1854s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1854s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1854s bt2 index files: $VAR1 = []; 1854s Note - bowtie-build indices do not yet exist. Indexing genome now. 1854s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1854s succeeded(23) 43.3962% completed. CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1854s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1854s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1854s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1854s 997 reads; of these: 1854s 997 (100.00%) were unpaired; of these: 1854s 3 (0.30%) aligned 0 times 1854s 568 (56.97%) aligned exactly 1 time 1854s 426 (42.73%) aligned >1 times 1854s 99.70% overall alignment rate 1854s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1854s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1854s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1854s bt2 index files: $VAR1 = []; 1854s Note - bowtie-build indices do not yet exist. Indexing genome now. 1854s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1854s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1854s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1854s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1854s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1854s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1854s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1855s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1855s 1855s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1855s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1855s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1855s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1855s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1855s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1855s -processing jaccard pair sensor 1855s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1855s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1855s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1855s [1000 lines read] scaff:a6;10 lend:1 rend:64 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1855s 70 reads; of these: 1855s 70 (100.00%) were unpaired; of these: 1855s 10 (14.29%) aligned 0 times 1855s 59 (84.29%) aligned exactly 1 time 1855s 1 (1.43%) aligned >1 times 1855s 85.71% overall alignment rate 1855s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1855s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1855s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads.out/inchworm.fa.clipped.fa 1855s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1855s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1855s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1855s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1855s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1855s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1855s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1855s 1855s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1855s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1855s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1855s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1855s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1855s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1855s -processing jaccard pair sensor 1855s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1855s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1855s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads.out/inchworm.fa.clipped.fa 1859s succeeded(24) 45.283% completed. succeeded(25) 47.1698% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1859s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1859s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1859s bt2 index files: $VAR1 = []; 1859s Note - bowtie-build indices do not yet exist. Indexing genome now. 1859s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1859s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1859s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1859s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1859s bt2 index files: $VAR1 = []; 1859s Note - bowtie-build indices do not yet exist. Indexing genome now. 1859s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1859s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1859s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1859s 10 reads; of these: 1859s 10 (100.00%) were unpaired; of these: 1859s 3 (30.00%) aligned 0 times 1859s 7 (70.00%) aligned exactly 1 time 1859s 0 (0.00%) aligned >1 times 1859s 70.00% overall alignment rate 1859s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1859s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1859s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1859s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1859s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1859s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1859s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1859s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1859s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1859s 1859s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1859s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1859s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1859s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1859s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1859s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1859s -processing jaccard pair sensor 1859s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1860s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1860s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads.out/inchworm.fa.clipped.fa 1860s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1860s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1860s 293 reads; of these: 1860s 293 (100.00%) were unpaired; of these: 1860s 0 (0.00%) aligned 0 times 1860s 293 (100.00%) aligned exactly 1 time 1860s 0 (0.00%) aligned >1 times 1860s 100.00% overall alignment rate 1860s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1860s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1860s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1860s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1860s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1860s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1860s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1860s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1860s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1860s 1860s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1860s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1860s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1860s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1860s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1860s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1860s -processing jaccard pair sensor 1860s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1860s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1860s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads.out/inchworm.fa.clipped.fa 1861s succeeded(26) 49.0566% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1861s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1861s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1861s bt2 index files: $VAR1 = []; 1861s Note - bowtie-build indices do not yet exist. Indexing genome now. 1861s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1861s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1861s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1861s 26 reads; of these: 1861s 26 (100.00%) were unpaired; of these: 1861s 6 (23.08%) aligned 0 times 1861s 20 (76.92%) aligned exactly 1 time 1861s 0 (0.00%) aligned >1 times 1861s 76.92% overall alignment rate 1861s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1861s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1861s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1861s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1861s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1861s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1861s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1861s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1861s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1861s 1861s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1861s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1861s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1861s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1861s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1861s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1861s -processing jaccard pair sensor 1861s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1861s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1861s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads.out/inchworm.fa.clipped.fa 1863s succeeded(27) 50.9434% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1863s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1863s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1863s bt2 index files: $VAR1 = []; 1863s Note - bowtie-build indices do not yet exist. Indexing genome now. 1863s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1864s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1864s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1864s 54 reads; of these: 1864s 54 (100.00%) were unpaired; of these: 1864s 9 (16.67%) aligned 0 times 1864s 45 (83.33%) aligned exactly 1 time 1864s 0 (0.00%) aligned >1 times 1864s 83.33% overall alignment rate 1864s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1864s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1864s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1864s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1864s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1864s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1864s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1864s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1864s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1864s 1864s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1864s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1864s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1864s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1864s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1864s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1864s -processing jaccard pair sensor 1864s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1864s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1864s succeeded(28) 52.8302% completed. CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads.out/inchworm.fa.clipped.fa 1864s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1864s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1864s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1864s bt2 index files: $VAR1 = []; 1864s Note - bowtie-build indices do not yet exist. Indexing genome now. 1864s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1865s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1865s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1865s 145 reads; of these: 1865s 145 (100.00%) were unpaired; of these: 1865s 1 (0.69%) aligned 0 times 1865s 144 (99.31%) aligned exactly 1 time 1865s 0 (0.00%) aligned >1 times 1865s 99.31% overall alignment rate 1865s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1865s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1865s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1865s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1865s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1865s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1865s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1865s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1865s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1865s 1865s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1865s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1865s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1865s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1865s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1865s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1865s -processing jaccard pair sensor 1865s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1865s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1865s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads.out/inchworm.fa.clipped.fa 1866s succeeded(29) 54.717% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1866s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1866s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1866s bt2 index files: $VAR1 = []; 1866s Note - bowtie-build indices do not yet exist. Indexing genome now. 1866s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1866s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1866s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1866s 16 reads; of these: 1866s 16 (100.00%) were unpaired; of these: 1866s 10 (62.50%) aligned 0 times 1866s 6 (37.50%) aligned exactly 1 time 1866s 0 (0.00%) aligned >1 times 1866s 37.50% overall alignment rate 1866s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1866s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1867s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1867s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1867s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1867s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1867s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1867s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1867s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1867s 1867s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1867s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1867s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1867s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1867s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1867s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1867s -processing jaccard pair sensor 1867s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1867s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1867s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads.out/inchworm.fa.clipped.fa 1868s succeeded(30) 56.6038% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1868s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1868s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1868s bt2 index files: $VAR1 = []; 1868s Note - bowtie-build indices do not yet exist. Indexing genome now. 1868s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1868s succeeded(31) 58.4906% completed. CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1868s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1869s 818 reads; of these: 1869s 818 (100.00%) were unpaired; of these: 1869s 1 (0.12%) aligned 0 times 1869s 758 (92.67%) aligned exactly 1 time 1869s 59 (7.21%) aligned >1 times 1869s 99.88% overall alignment rate 1869s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1869s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1869s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1869s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1869s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1869s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1869s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1869s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1869s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1869s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1869s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1869s 1869s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1869s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1869s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1869s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1869s bt2 index files: $VAR1 = []; 1869s Note - bowtie-build indices do not yet exist. Indexing genome now. 1869s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1869s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1869s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1869s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1869s -processing jaccard pair sensor 1869s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1869s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1869s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads.out/inchworm.fa.clipped.fa 1869s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1869s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1870s 3962 reads; of these: 1870s 3962 (100.00%) were unpaired; of these: 1870s 2 (0.05%) aligned 0 times 1870s 2253 (56.87%) aligned exactly 1 time 1870s 1707 (43.08%) aligned >1 times 1870s 99.95% overall alignment rate 1870s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1870s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1870s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1870s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1870s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam 1870s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam 1870s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1870s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam 1870s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1870s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1870s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1870s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1870s 1870s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1870s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1870s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1870s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1870s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1870s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1870s -processing jaccard pair sensor 1871s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1871s [1000 lines read] scaff:a21;2 lend:1 rend:35 [2000 lines read] scaff:a38;2 lend:1 rend:49 [3000 lines read] scaff:a3;145 lend:155 rend:222 [4000 lines read] scaff:a4;148 lend:1 rend:68 [5000 lines read] scaff:a5;138 lend:67 rend:134 [6000 lines read] scaff:a8;8 lend:26 rend:93 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1871s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads.out/inchworm.fa.clipped.fa 1873s succeeded(32) 60.3774% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1873s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1873s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1873s bt2 index files: $VAR1 = []; 1873s Note - bowtie-build indices do not yet exist. Indexing genome now. 1873s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1874s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1874s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1874s 26 reads; of these: 1874s 26 (100.00%) were unpaired; of these: 1874s 0 (0.00%) aligned 0 times 1874s 26 (100.00%) aligned exactly 1 time 1874s 0 (0.00%) aligned >1 times 1874s 100.00% overall alignment rate 1874s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1874s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1874s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1874s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1874s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1874s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1874s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1874s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1874s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1874s 1874s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1874s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1874s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1874s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1874s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1874s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1874s -processing jaccard pair sensor 1874s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1874s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1874s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads.out/inchworm.fa.clipped.fa 1876s succeeded(33) 62.2641% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1876s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1876s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1876s bt2 index files: $VAR1 = []; 1876s Note - bowtie-build indices do not yet exist. Indexing genome now. 1876s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1877s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1877s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1877s 27 reads; of these: 1877s 27 (100.00%) were unpaired; of these: 1877s 6 (22.22%) aligned 0 times 1877s 21 (77.78%) aligned exactly 1 time 1877s 0 (0.00%) aligned >1 times 1877s 77.78% overall alignment rate 1877s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1877s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1877s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1877s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1877s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1877s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1877s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1877s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1877s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1877s 1877s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1877s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1877s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1877s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1877s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1877s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1877s -processing jaccard pair sensor 1877s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1877s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1877s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads.out/inchworm.fa.clipped.fa 1877s succeeded(34) 64.1509% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1877s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1877s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1877s bt2 index files: $VAR1 = []; 1877s Note - bowtie-build indices do not yet exist. Indexing genome now. 1877s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1878s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1878s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1878s 16 reads; of these: 1878s 16 (100.00%) were unpaired; of these: 1878s 0 (0.00%) aligned 0 times 1878s 14 (87.50%) aligned exactly 1 time 1878s 2 (12.50%) aligned >1 times 1878s 100.00% overall alignment rate 1878s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1878s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1878s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1878s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1878s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1878s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1878s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1878s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1878s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1878s 1878s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1878s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1878s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1878s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1878s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1878s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1878s -processing jaccard pair sensor 1878s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1878s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1878s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads.out/inchworm.fa.clipped.fa 1879s succeeded(35) 66.0377% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1879s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1879s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1879s bt2 index files: $VAR1 = []; 1879s Note - bowtie-build indices do not yet exist. Indexing genome now. 1879s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1879s succeeded(36) 67.9245% completed. CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1879s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1879s 371 reads; of these: 1879s 371 (100.00%) were unpaired; of these: 1879s 2 (0.54%) aligned 0 times 1879s 296 (79.78%) aligned exactly 1 time 1879s 73 (19.68%) aligned >1 times 1879s 99.46% overall alignment rate 1879s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1879s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1879s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1879s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1879s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1879s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1879s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1879s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1879s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1879s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1879s bt2 index files: $VAR1 = []; 1879s Note - bowtie-build indices do not yet exist. Indexing genome now. 1879s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1879s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1879s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1879s 1879s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1879s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1879s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1879s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1879s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1879s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1879s -processing jaccard pair sensor 1879s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1879s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1879s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads.out/inchworm.fa.clipped.fa 1879s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1879s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1880s 26 reads; of these: 1880s 26 (100.00%) were unpaired; of these: 1880s 17 (65.38%) aligned 0 times 1880s 9 (34.62%) aligned exactly 1 time 1880s 0 (0.00%) aligned >1 times 1880s 34.62% overall alignment rate 1880s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1880s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1880s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1880s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1880s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1880s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1880s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1880s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1880s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1880s 1880s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1880s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1880s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1880s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1880s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1880s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1880s -processing jaccard pair sensor 1880s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1880s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1880s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads.out/inchworm.fa.clipped.fa 1882s succeeded(37) 69.8113% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1882s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1882s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1882s bt2 index files: $VAR1 = []; 1882s Note - bowtie-build indices do not yet exist. Indexing genome now. 1882s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1882s succeeded(38) 71.6981% completed. CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1882s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1883s 1811 reads; of these: 1883s 1811 (100.00%) were unpaired; of these: 1883s 6 (0.33%) aligned 0 times 1883s 1189 (65.65%) aligned exactly 1 time 1883s 616 (34.01%) aligned >1 times 1883s 99.67% overall alignment rate 1883s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1883s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1883s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1883s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1883s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1883s bt2 index files: $VAR1 = []; 1883s Note - bowtie-build indices do not yet exist. Indexing genome now. 1883s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1883s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1883s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1883s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1883s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1883s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1883s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1883s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1883s 1883s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1883s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1883s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1883s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1883s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1883s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1883s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1883s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1883s -processing jaccard pair sensor 1883s 52 reads; of these: 1883s 52 (100.00%) were unpaired; of these: 1883s 5 (9.62%) aligned 0 times 1883s 47 (90.38%) aligned exactly 1 time 1883s 0 (0.00%) aligned >1 times 1883s 90.38% overall alignment rate 1883s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1883s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1883s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1883s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1883s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1883s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1883s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1883s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1883s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1883s [1000 lines read] scaff:a1;56 lend:769 rend:1089 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1883s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1883s 1883s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1883s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1883s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1883s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1883s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads.out/inchworm.fa.clipped.fa 1883s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1883s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1883s -processing jaccard pair sensor 1883s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1883s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1883s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads.out/inchworm.fa.clipped.fa 1887s succeeded(39) 73.5849% completed. succeeded(40) 75.4717% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1887s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1887s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1887s bt2 index files: $VAR1 = []; 1887s Note - bowtie-build indices do not yet exist. Indexing genome now. 1887s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1887s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1887s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1887s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1887s bt2 index files: $VAR1 = []; 1887s Note - bowtie-build indices do not yet exist. Indexing genome now. 1887s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1887s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1887s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1887s 538 reads; of these: 1887s 538 (100.00%) were unpaired; of these: 1887s 2 (0.37%) aligned 0 times 1887s 530 (98.51%) aligned exactly 1 time 1887s 6 (1.12%) aligned >1 times 1887s 99.63% overall alignment rate 1887s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1887s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1887s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1887s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1887s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1887s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1887s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1887s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1887s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1887s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1887s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1887s 1887s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1887s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1887s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1887s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1887s 907 reads; of these: 1887s 907 (100.00%) were unpaired; of these: 1887s 2 (0.22%) aligned 0 times 1887s 839 (92.50%) aligned exactly 1 time 1887s 66 (7.28%) aligned >1 times 1887s 99.78% overall alignment rate 1887s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1887s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1887s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1887s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1887s -processing jaccard pair sensor 1887s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1888s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1888s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1888s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1888s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1888s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1888s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1888s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1888s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads.out/inchworm.fa.clipped.fa 1888s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1888s 1888s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1888s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1888s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1888s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1888s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1888s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1888s -processing jaccard pair sensor 1888s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1888s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1888s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads.out/inchworm.fa.clipped.fa 1891s succeeded(41) 77.3585% completed. succeeded(42) 79.2453% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1891s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1892s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1892s bt2 index files: $VAR1 = []; 1892s Note - bowtie-build indices do not yet exist. Indexing genome now. 1892s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1892s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1892s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1892s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1892s bt2 index files: $VAR1 = []; 1892s Note - bowtie-build indices do not yet exist. Indexing genome now. 1892s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1892s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1892s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1892s 18 reads; of these: 1892s 18 (100.00%) were unpaired; of these: 1892s 1 (5.56%) aligned 0 times 1892s 17 (94.44%) aligned exactly 1 time 1892s 0 (0.00%) aligned >1 times 1892s 94.44% overall alignment rate 1892s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1892s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1892s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1892s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1892s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1892s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1892s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1892s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1892s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1892s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1892s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1892s 1892s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1892s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1892s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1892s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1892s 18 reads; of these: 1892s 18 (100.00%) were unpaired; of these: 1892s 5 (27.78%) aligned 0 times 1892s 13 (72.22%) aligned exactly 1 time 1892s 0 (0.00%) aligned >1 times 1892s 72.22% overall alignment rate 1892s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1892s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1892s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1892s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1892s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1892s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1892s -processing jaccard pair sensor 1892s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1892s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1892s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1892s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1892s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1892s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1892s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads.out/inchworm.fa.clipped.fa 1892s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1892s 1892s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1892s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1892s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1892s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1892s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1892s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1892s -processing jaccard pair sensor 1892s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1892s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1892s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads.out/inchworm.fa.clipped.fa 1894s succeeded(43) 81.1321% completed. succeeded(44) 83.0189% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1894s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1894s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1894s bt2 index files: $VAR1 = []; 1894s Note - bowtie-build indices do not yet exist. Indexing genome now. 1894s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1894s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1894s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1894s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1894s bt2 index files: $VAR1 = []; 1894s Note - bowtie-build indices do not yet exist. Indexing genome now. 1894s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1894s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1894s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1894s 76 reads; of these: 1894s 76 (100.00%) were unpaired; of these: 1894s 0 (0.00%) aligned 0 times 1894s 76 (100.00%) aligned exactly 1 time 1894s 0 (0.00%) aligned >1 times 1894s 100.00% overall alignment rate 1894s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1894s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1894s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1894s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1894s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1894s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1894s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1894s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1894s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1894s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1894s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1894s 1894s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1894s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1894s 42 reads; of these: 1894s 42 (100.00%) were unpaired; of these: 1894s 18 (42.86%) aligned 0 times 1894s 24 (57.14%) aligned exactly 1 time 1894s 0 (0.00%) aligned >1 times 1894s 57.14% overall alignment rate 1894s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1894s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1894s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1894s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1894s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1894s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1894s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1894s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1894s -processing jaccard pair sensor 1894s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1894s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1894s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1894s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1894s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1894s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1894s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads.out/inchworm.fa.clipped.fa 1895s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1895s 1895s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1895s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1895s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1895s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1895s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1895s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1895s -processing jaccard pair sensor 1895s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1895s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1895s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads.out/inchworm.fa.clipped.fa 1896s succeeded(45) 84.9057% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1896s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1896s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1896s bt2 index files: $VAR1 = []; 1896s Note - bowtie-build indices do not yet exist. Indexing genome now. 1896s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1897s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1897s succeeded(46) 86.7924% completed. CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1897s 4380 reads; of these: 1897s 4380 (100.00%) were unpaired; of these: 1897s 10 (0.23%) aligned 0 times 1897s 2462 (56.21%) aligned exactly 1 time 1897s 1908 (43.56%) aligned >1 times 1897s 99.77% overall alignment rate 1897s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1897s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1897s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1897s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1897s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1897s bt2 index files: $VAR1 = []; 1897s Note - bowtie-build indices do not yet exist. Indexing genome now. 1897s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1897s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1898s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1898s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam 1898s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam 1898s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1898s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam 1898s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1898s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1898s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1898s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1898s 1898s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1898s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1898s 953 reads; of these: 1898s 953 (100.00%) were unpaired; of these: 1898s 4 (0.42%) aligned 0 times 1898s 555 (58.24%) aligned exactly 1 time 1898s 394 (41.34%) aligned >1 times 1898s 99.58% overall alignment rate 1898s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1898s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1898s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1898s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1898s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1898s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1898s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1898s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1898s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1898s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1898s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1898s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1898s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1898s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1898s 1898s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1898s -processing jaccard pair sensor 1898s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1898s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1898s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1898s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1898s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1898s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1898s -processing jaccard pair sensor 1898s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1898s [1000 lines read] scaff:a7;10 lend:1 rend:54 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1898s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads.out/inchworm.fa.clipped.fa 1898s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1898s [1000 lines read] scaff:a1;135 lend:78 rend:364 [2000 lines read] scaff:a1;135 lend:614 rend:934 [3000 lines read] scaff:a20;2 lend:7 rend:49 [4000 lines read] scaff:a34;2 lend:1 rend:36 [5000 lines read] scaff:a5;2 lend:1 rend:43 CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1898s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads.out/inchworm.fa.clipped.fa 1903s succeeded(47) 88.6792% completed. succeeded(48) 90.566% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1903s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1903s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1903s bt2 index files: $VAR1 = []; 1903s Note - bowtie-build indices do not yet exist. Indexing genome now. 1903s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1904s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1904s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1904s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1904s bt2 index files: $VAR1 = []; 1904s Note - bowtie-build indices do not yet exist. Indexing genome now. 1904s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1904s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1904s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1904s 20 reads; of these: 1904s 20 (100.00%) were unpaired; of these: 1904s 4 (20.00%) aligned 0 times 1904s 16 (80.00%) aligned exactly 1 time 1904s 0 (0.00%) aligned >1 times 1904s 80.00% overall alignment rate 1904s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1904s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1904s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1904s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1904s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1904s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1904s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1904s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1904s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1904s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1904s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1904s 1904s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1904s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1904s 98 reads; of these: 1904s 98 (100.00%) were unpaired; of these: 1904s 0 (0.00%) aligned 0 times 1904s 98 (100.00%) aligned exactly 1 time 1904s 0 (0.00%) aligned >1 times 1904s 100.00% overall alignment rate 1904s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1904s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1904s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1904s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1904s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1904s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1904s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1904s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1904s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1904s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1904s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1904s -processing jaccard pair sensor 1904s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1904s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1904s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1904s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads.out/inchworm.fa.clipped.fa 1904s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1904s 1904s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1904s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1904s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1904s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1904s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1904s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1904s -processing jaccard pair sensor 1904s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1904s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1904s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads.out/inchworm.fa.clipped.fa 1906s succeeded(49) 92.4528% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1906s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1906s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1906s bt2 index files: $VAR1 = []; 1906s Note - bowtie-build indices do not yet exist. Indexing genome now. 1906s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1906s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1906s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1907s 85 reads; of these: 1907s 85 (100.00%) were unpaired; of these: 1907s 6 (7.06%) aligned 0 times 1907s 79 (92.94%) aligned exactly 1 time 1907s 0 (0.00%) aligned >1 times 1907s 92.94% overall alignment rate 1907s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1907s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1907s succeeded(50) 94.3396% completed. CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1907s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1907s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1907s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1907s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1907s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1907s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1907s 1907s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1907s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1907s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1907s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1907s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1907s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1907s -processing jaccard pair sensor 1907s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1907s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1907s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads.out/inchworm.fa.clipped.fa 1907s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1907s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1907s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1907s bt2 index files: $VAR1 = []; 1907s Note - bowtie-build indices do not yet exist. Indexing genome now. 1907s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1907s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1907s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1907s 10 reads; of these: 1907s 10 (100.00%) were unpaired; of these: 1907s 5 (50.00%) aligned 0 times 1907s 5 (50.00%) aligned exactly 1 time 1907s 0 (0.00%) aligned >1 times 1907s 50.00% overall alignment rate 1907s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1907s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1907s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1907s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1907s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1907s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1907s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1907s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1907s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1907s 1907s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1907s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1907s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1907s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1907s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1907s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1907s -processing jaccard pair sensor 1907s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1907s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1907s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads.out/inchworm.fa.clipped.fa 1909s succeeded(51) 96.2264% completed. CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/inchworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1909s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads --CPU 1 --target /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/iworm.fa -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 1909s CMD: samtools faidx /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1909s bt2 index files: $VAR1 = []; 1909s Note - bowtie-build indices do not yet exist. Indexing genome now. 1909s CMD: bowtie2-build -q /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/iworm.fa /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/iworm.fa 1909s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok 1909s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/iworm.fa -U /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 1910s 46 reads; of these: 1910s 46 (100.00%) were unpaired; of these: 1910s 0 (0.00%) aligned 0 times 1910s 44 (95.65%) aligned exactly 1 time 1910s 2 (4.35%) aligned >1 times 1910s 100.00% overall alignment rate 1910s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok 1910s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F 1910s CMD: samtools view -bt /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/iworm.fa.fai /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam | samtools sort -o - - > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1910s CMD: samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam 1910s -cleaning up and removing intermediate file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam 1910s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam 1910s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig 1910s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 1910s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords 1910s 1910s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok 1910s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1910s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname 1910s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted 1910s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100 --pseudocounts 1 1910s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend 1910s -processing jaccard pair sensor 1910s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig 1910s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig > bowtie_alignments.for_jaccard.bam.J100.wig.clips 1910s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/inchworm.fa bowtie_alignments.for_jaccard.bam.J100.wig.clips > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads.out/inchworm.fa.clipped.fa 1912s succeeded(52) 98.1132% completed. succeeded(53) 100% completed. 1912s 1912s All commands completed successfully. :-) 1912s 1912s Saturday, November 2, 2024: 18:08:48 CMD: find Dir_* -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta.tmp 1912s Saturday, November 2, 2024: 18:08:48 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta.gene_trans_map 1912s 1912s 1912s Finished. See /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta for reconstructed transcripts 1912s 1912s 1912s outfile="test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta" 1912s asmsize=$(wc -c <"${outfile}") 1912s if [ $asmsize -le 50000 ]; then 1912s echo "Error, ${outfile} potentially incomplete" 1912s exit 1 1912s else 1912s echo "ok" 1912s exit 0 1912s fi 1912s ok 1912s ./run_small_GG_mutliScaff_test.sh 1912s #!/bin/bash -ve 1912s 1912s 1912s $TRINITY_HOME/Trinity --genome_guided_max_intron 1000 --genome_guided_bam transAligns.cSorted.bam --max_memory 2G --output test_GG_use_small_multiscaff_bam_trinity_outdir 1912s 1912s 1912s ______ ____ ____ ____ ____ ______ __ __ 1912s | || \ | || \ | || || | | 1912s | || D ) | | | _ | | | | || | | 1912s |_| |_|| / | | | | | | | |_| |_|| ~ | 1912s | | | \ | | | | | | | | | |___, | 1912s | | | . \ | | | | | | | | | | | 1912s |__| |__|\_||____||__|__||____| |__| |____/ 1912s 1912s Trinity-v2.15.1 1912s 1912s 1912s 1912s Saturday, November 2, 2024: 18:08:48 CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl transAligns.cSorted.bam 1912s -appears to be a coordinate sorted bam file. ok. 1912s Saturday, November 2, 2024: 18:08:48 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir 1912s 1912s 1912s ---------------------------------------------------------------------------------- 1912s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 1912s ---------------------------------------------------------------------------------- 1912s 1912s -found paired-end aligned read. Running in paired-end mode. 1912s Saturday, November 2, 2024: 18:08:48 CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/transAligns.cSorted.bam.norm_200.bam --keep_secondary /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/transAligns.cSorted.bam 1915s Done with chr TRINITY_DN0_c0_g1_i1. 1915s Done with chr TRINITY_DN10_c0_g1_i1. 1915s Done with chr TRINITY_DN12_c0_g1_i1. 1915s Done with chr TRINITY_DN12_c0_g1_i2. 1915s Done with chr TRINITY_DN14_c0_g1_i1. 1915s Done with chr TRINITY_DN14_c0_g2_i1. 1915s Done with chr TRINITY_DN15_c0_g1_i1. 1915s Done with chr TRINITY_DN16_c0_g1_i1. 1915s Done with chr TRINITY_DN16_c0_g2_i1. 1915s Done with chr TRINITY_DN18_c0_g1_i1. 1915s Done with chr TRINITY_DN18_c0_g1_i2. 1915s Done with chr TRINITY_DN19_c0_g1_i1. 1915s Done with chr TRINITY_DN20_c0_g1_i1. 1915s Done with chr TRINITY_DN20_c0_g2_i1. 1915s Done with chr TRINITY_DN20_c0_g1_i2. 1915s Done with chr TRINITY_DN20_c0_g1_i3. 1915s Done with chr TRINITY_DN20_c0_g1_i4. 1915s Done with chr TRINITY_DN20_c0_g1_i5. 1915s Done with chr TRINITY_DN20_c0_g1_i6. 1915s Done with chr TRINITY_DN20_c0_g1_i7. 1915s Done with chr TRINITY_DN21_c0_g1_i1. 1915s Done with chr TRINITY_DN21_c0_g1_i2. 1915s Done with chr TRINITY_DN22_c0_g1_i1. 1915s Done with chr TRINITY_DN22_c0_g2_i1. 1915s Done with chr TRINITY_DN22_c0_g3_i1. 1915s Done with chr TRINITY_DN22_c0_g4_i1. 1915s Done with chr TRINITY_DN22_c0_g3_i2. 1915s Done with chr TRINITY_DN22_c0_g3_i3. 1915s Done with chr TRINITY_DN22_c0_g3_i4. 1915s Done with chr TRINITY_DN22_c0_g5_i1. 1915s Done with chr TRINITY_DN22_c0_g6_i1. 1915s Done with chr TRINITY_DN22_c0_g3_i5. 1915s Done with chr TRINITY_DN22_c0_g7_i1. 1915s Done with chr TRINITY_DN23_c0_g1_i1. 1915s Done with chr TRINITY_DN23_c0_g2_i1. 1915s Done with chr TRINITY_DN23_c0_g1_i2. 1915s Done with chr TRINITY_DN23_c0_g3_i1. 1915s Done with chr TRINITY_DN23_c0_g4_i1. 1915s Done with chr TRINITY_DN23_c0_g5_i1. 1915s Done with chr TRINITY_DN23_c0_g1_i3. 1915s Done with chr TRINITY_DN23_c0_g1_i4. 1915s Done with chr TRINITY_DN24_c0_g1_i1. 1915s Done with chr TRINITY_DN24_c0_g2_i1. 1915s Done with chr TRINITY_DN24_c0_g3_i1. 1915s Done with chr TRINITY_DN24_c0_g3_i2. 1915s Done with chr TRINITY_DN25_c1_g1_i1. 1915s Done with chr TRINITY_DN25_c1_g1_i2. 1915s Done with chr TRINITY_DN25_c1_g1_i3. 1915s Done with chr TRINITY_DN25_c1_g1_i4. 1915s Done with chr TRINITY_DN25_c1_g1_i5. 1915s Done with chr TRINITY_DN26_c0_g1_i1. 1915s Done with chr TRINITY_DN26_c0_g1_i2. 1915s Done with chr TRINITY_DN26_c1_g1_i1. 1915s Done with chr TRINITY_DN26_c1_g1_i2. 1915s Done with chr TRINITY_DN26_c1_g1_i3. 1915s Done with chr TRINITY_DN26_c1_g1_i4. 1915s Done with chr TRINITY_DN26_c1_g1_i5. 1915s Done with chr TRINITY_DN26_c1_g1_i6. 1915s Done with chr TRINITY_DN26_c1_g2_i1. 1915s Done with chr TRINITY_DN26_c1_g1_i7. 1915s Done with chr TRINITY_DN26_c1_g3_i1. 1915s Done with chr TRINITY_DN26_c1_g1_i8. 1915s Done with chr TRINITY_DN26_c1_g1_i9. 1915s Done with chr TRINITY_DN26_c1_g1_i10. 1915s Done with chr TRINITY_DN26_c1_g1_i11. 1915s Done with chr TRINITY_DN26_c1_g3_i2. 1915s Done with chr TRINITY_DN26_c1_g1_i12. 1915s Done with chr TRINITY_DN26_c1_g4_i1. 1915s Done with chr TRINITY_DN26_c1_g1_i13. 1915s Done with chr TRINITY_DN26_c1_g1_i14. 1915s Done with chr TRINITY_DN26_c1_g1_i15. 1915s Done with chr TRINITY_DN26_c1_g1_i16. 1915s Done with chr TRINITY_DN26_c1_g1_i17. 1915s Done with chr TRINITY_DN26_c1_g1_i18. 1915s Done with chr TRINITY_DN26_c1_g3_i3. 1915s Done with chr TRINITY_DN26_c1_g1_i19. 1915s Done with chr TRINITY_DN26_c1_g3_i4. 1915s Done with chr TRINITY_DN26_c1_g5_i1. 1915s Done with chr TRINITY_DN26_c1_g1_i20. 1915s Done with chr TRINITY_DN26_c1_g1_i21. 1915s Done with chr TRINITY_DN26_c1_g3_i5. 1915s Done with chr TRINITY_DN26_c2_g1_i1. 1915s Done with chr TRINITY_DN26_c2_g1_i2. 1915s Done with chr TRINITY_DN26_c2_g2_i1. 1915s Done with chr TRINITY_DN26_c2_g3_i1. 1915s Done with chr TRINITY_DN26_c2_g1_i3. 1915s Done with chr TRINITY_DN26_c2_g1_i4. 1915s Done with chr TRINITY_DN26_c2_g1_i5. 1915s Done with chr TRINITY_DN27_c0_g1_i1. 1915s Done with chr TRINITY_DN4_c0_g1_i1. 1915s Done with chr TRINITY_DN5_c0_g1_i1. 1915s Saturday, November 2, 2024: 18:08:51 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/transAligns.cSorted.bam.norm_200.bam.ok 1915s Saturday, November 2, 2024: 18:08:51 CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/transAligns.cSorted.bam.norm_200.bam -I 1000 --sort_buffer 2G --CPU 2 1915s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --CPU 2 --sort_buffer 2G --sam transAligns.cSorted.bam.norm_200.bam --min_insert_size 1 --max_insert_size 1000 1915s -extracting read coordinates from transAligns.cSorted.bam.norm_200.bam into transAligns.cSorted.bam.norm_200.bam.read_coords 1915s 1922s CMD: touch transAligns.cSorted.bam.norm_200.bam.read_coords.ok 1922s CMD: /usr/bin/sort --parallel=2 -S2G -T . -k1,1 -k2,2 -k4,4n transAligns.cSorted.bam.norm_200.bam.read_coords > transAligns.cSorted.bam.norm_200.bam.read_coords.sort_by_readname 1922s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/transAligns.cSorted.bam.norm_200.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/transAligns.cSorted.bam.norm_200.bam.read_coords.sort_by_readname 1923s CMD: /usr/bin/sort --parallel=2 -S2G -T . -k1,1 -k3,3n transAligns.cSorted.bam.norm_200.bam.frag_coords > transAligns.cSorted.bam.norm_200.bam.frag_coords.coord_sorted 1924s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl transAligns.cSorted.bam.norm_200.bam.frag_coords > transAligns.cSorted.bam.norm_200.bam.frag_coverage.wig 1928s [1000 lines read] scaff:TRINITY_DN20_c0_g1_i3 lend:239 rend:679 [2000 lines read] scaff:TRINITY_DN20_c0_g1_i4 lend:1507 rend:1760 [3000 lines read] scaff:TRINITY_DN20_c0_g1_i6 lend:1153 rend:1530 [4000 lines read] scaff:TRINITY_DN20_c0_g1_i7 lend:2556 rend:2779 [5000 lines read] scaff:TRINITY_DN21_c0_g1_i2 lend:2348 rend:2568 [6000 lines read] scaff:TRINITY_DN22_c0_g3_i1 lend:829 rend:1294 [7000 lines read] scaff:TRINITY_DN22_c0_g3_i1 lend:1692 rend:2029 [8000 lines read] scaff:TRINITY_DN22_c0_g3_i3 lend:157 rend:523 [9000 lines read] scaff:TRINITY_DN22_c0_g3_i3 lend:1182 rend:1523 [10000 lines read] scaff:TRINITY_DN22_c0_g3_i3 lend:1902 rend:2126 [11000 lines read] scaff:TRINITY_DN22_c0_g3_i4 lend:1028 rend:1456 [12000 lines read] scaff:TRINITY_DN22_c0_g3_i4 lend:1758 rend:1956 [13000 lines read] scaff:TRINITY_DN22_c0_g3_i5 lend:948 rend:1211 [14000 lines read] scaff:TRINITY_DN22_c0_g3_i5 lend:1737 rend:1980 [15000 lines read] scaff:TRINITY_DN23_c0_g1_i2 lend:706 rend:1098 [16000 lines read] scaff:TRINITY_DN23_c0_g1_i3 lend:463 rend:897 [17000 lines read] scaff:TRINITY_DN24_c0_g1_i1 lend:21 rend:96 [18000 lines read] scaff:TRINITY_DN24_c0_g3_i1 lend:2084 rend:2302 [19000 lines read] scaff:TRINITY_DN24_c0_g3_i1 lend:3550 rend:3977 [20000 lines read] scaff:TRINITY_DN24_c0_g3_i1 lend:4820 rend:5143 [21000 lines read] scaff:TRINITY_DN24_c0_g3_i1 lend:5830 rend:6117 [22000 lines read] scaff:TRINITY_DN24_c0_g3_i1 lend:6807 rend:7101 [23000 lines read] scaff:TRINITY_DN25_c1_g1_i1 lend:348 rend:648 [24000 lines read] scaff:TRINITY_DN25_c1_g1_i2 lend:106 rend:469 [25000 lines read] scaff:TRINITY_DN25_c1_g1_i2 lend:699 rend:940 [26000 lines read] scaff:TRINITY_DN25_c1_g1_i2 lend:1478 rend:1730 [27000 lines read] scaff:TRINITY_DN25_c1_g1_i2 lend:2198 rend:2415 [28000 lines read] scaff:TRINITY_DN25_c1_g1_i2 lend:2932 rend:3417 [29000 lines read] scaff:TRINITY_DN25_c1_g1_i3 lend:172 rend:350 [30000 lines read] scaff:TRINITY_DN25_c1_g1_i3 lend:860 rend:1098 [31000 lines read] scaff:TRINITY_DN25_c1_g1_i3 lend:1632 rend:2117 [32000 lines read] scaff:TRINITY_DN25_c1_g1_i3 lend:2355 rend:2639 [33000 lines read] scaff:TRINITY_DN25_c1_g1_i3 lend:3089 rend:3401 [34000 lines read] scaff:TRINITY_DN25_c1_g1_i4 lend:179 rend:396 [35000 lines read] scaff:TRINITY_DN25_c1_g1_i4 lend:883 rend:1108 [36000 lines read] scaff:TRINITY_DN25_c1_g1_i4 lend:1649 rend:2110 [37000 lines read] scaff:TRINITY_DN25_c1_g1_i4 lend:2375 rend:2701 [38000 lines read] scaff:TRINITY_DN25_c1_g1_i4 lend:3111 rend:3471 [39000 lines read] scaff:TRINITY_DN26_c0_g1_i1 lend:1083 rend:1530 [40000 lines read] scaff:TRINITY_DN26_c0_g1_i1 lend:3886 rend:4099 [41000 lines read] scaff:TRINITY_DN26_c0_g1_i2 lend:2009 rend:2185 [42000 lines read] scaff:TRINITY_DN26_c0_g1_i2 lend:5292 rend:5468 [43000 lines read] scaff:TRINITY_DN26_c1_g1_i1 lend:3670 rend:3941 [44000 lines read] scaff:TRINITY_DN26_c1_g1_i1 lend:6356 rend:6724 [45000 lines read] scaff:TRINITY_DN26_c1_g1_i10 lend:917 rend:1161 [46000 lines read] scaff:TRINITY_DN26_c1_g1_i10 lend:4502 rend:4753 [47000 lines read] scaff:TRINITY_DN26_c1_g1_i10 lend:7064 rend:7139 [48000 lines read] scaff:TRINITY_DN26_c1_g1_i11 lend:1958 rend:2158 [49000 lines read] scaff:TRINITY_DN26_c1_g1_i11 lend:5030 rend:5273 [50000 lines read] scaff:TRINITY_DN26_c1_g1_i12 lend:2479 rend:2741 [51000 lines read] scaff:TRINITY_DN26_c1_g1_i12 lend:5516 rend:5882 [52000 lines read] scaff:TRINITY_DN26_c1_g1_i12 lend:7708 rend:8081 [53000 lines read] scaff:TRINITY_DN26_c1_g1_i13 lend:3311 rend:3522 [54000 lines read] scaff:TRINITY_DN26_c1_g1_i13 lend:6051 rend:6401 [55000 lines read] scaff:TRINITY_DN26_c1_g1_i14 lend:491 rend:724 [56000 lines read] scaff:TRINITY_DN26_c1_g1_i14 lend:4077 rend:4301 [57000 lines read] scaff:TRINITY_DN26_c1_g1_i14 lend:6738 rend:6933 [58000 lines read] scaff:TRINITY_DN26_c1_g1_i15 lend:1550 rend:2012 [59000 lines read] scaff:TRINITY_DN26_c1_g1_i15 lend:4771 rend:4846 [60000 lines read] scaff:TRINITY_DN26_c1_g1_i15 lend:7318 rend:7576 [61000 lines read] scaff:TRINITY_DN26_c1_g1_i16 lend:2570 rend:2757 [62000 lines read] scaff:TRINITY_DN26_c1_g1_i16 lend:5596 rend:5899 [63000 lines read] scaff:TRINITY_DN26_c1_g1_i16 lend:7788 rend:8031 [64000 lines read] scaff:TRINITY_DN26_c1_g1_i17 lend:3454 rend:3833 [65000 lines read] scaff:TRINITY_DN26_c1_g1_i17 lend:6209 rend:6523 [66000 lines read] scaff:TRINITY_DN26_c1_g1_i18 lend:639 rend:1145 [67000 lines read] scaff:TRINITY_DN26_c1_g1_i18 lend:4280 rend:4782 [68000 lines read] scaff:TRINITY_DN26_c1_g1_i18 lend:6870 rend:7061 [69000 lines read] scaff:TRINITY_DN26_c1_g1_i19 lend:1781 rend:2159 [70000 lines read] scaff:TRINITY_DN26_c1_g1_i19 lend:4977 rend:5000 [71000 lines read] scaff:TRINITY_DN26_c1_g1_i2 lend:1904 rend:2258 [72000 lines read] scaff:TRINITY_DN26_c1_g1_i2 lend:5014 rend:5341 [73000 lines read] scaff:TRINITY_DN26_c1_g1_i2 lend:7475 rend:7729 [74000 lines read] scaff:TRINITY_DN26_c1_g1_i20 lend:2908 rend:3109 [75000 lines read] scaff:TRINITY_DN26_c1_g1_i20 lend:5787 rend:6209 [76000 lines read] scaff:TRINITY_DN26_c1_g1_i20 lend:7967 rend:8042 [77000 lines read] scaff:TRINITY_DN26_c1_g1_i21 lend:3555 rend:3822 [78000 lines read] scaff:TRINITY_DN26_c1_g1_i3 lend:415 rend:702 [79000 lines read] scaff:TRINITY_DN26_c1_g1_i3 lend:4010 rend:4297 [80000 lines read] scaff:TRINITY_DN26_c1_g1_i3 lend:6763 rend:7122 [81000 lines read] scaff:TRINITY_DN26_c1_g1_i4 lend:1553 rend:1772 [82000 lines read] scaff:TRINITY_DN26_c1_g1_i4 lend:4772 rend:4847 [83000 lines read] scaff:TRINITY_DN26_c1_g1_i4 lend:7340 rend:7721 [84000 lines read] scaff:TRINITY_DN26_c1_g1_i5 lend:2538 rend:2988 [85000 lines read] scaff:TRINITY_DN26_c1_g1_i5 lend:5541 rend:5960 [86000 lines read] scaff:TRINITY_DN26_c1_g1_i5 lend:7740 rend:8038 [87000 lines read] scaff:TRINITY_DN26_c1_g1_i6 lend:3490 rend:3730 [88000 lines read] scaff:TRINITY_DN26_c1_g1_i6 lend:6205 rend:6497 [89000 lines read] scaff:TRINITY_DN26_c1_g1_i7 lend:631 rend:918 [90000 lines read] scaff:TRINITY_DN26_c1_g1_i7 lend:4279 rend:4599 [91000 lines read] scaff:TRINITY_DN26_c1_g1_i7 lend:6844 rend:7088 [92000 lines read] scaff:TRINITY_DN26_c1_g1_i8 lend:1731 rend:1973 [93000 lines read] scaff:TRINITY_DN26_c1_g1_i8 lend:4917 rend:4940 [94000 lines read] scaff:TRINITY_DN26_c1_g1_i8 lend:7416 rend:7628 [95000 lines read] scaff:TRINITY_DN26_c1_g1_i9 lend:2864 rend:3179 [96000 lines read] scaff:TRINITY_DN26_c1_g1_i9 lend:5771 rend:6205 [97000 lines read] scaff:TRINITY_DN26_c1_g1_i9 lend:7872 rend:8074 [98000 lines read] scaff:TRINITY_DN26_c1_g3_i1 lend:1725 rend:2172 [99000 lines read] scaff:TRINITY_DN26_c1_g3_i1 lend:3369 rend:3556 [100000 lines read] scaff:TRINITY_DN26_c1_g3_i1 lend:4963 rend:5166 [101000 lines read] scaff:TRINITY_DN26_c1_g3_i2 lend:730 rend:1055 [102000 lines read] scaff:TRINITY_DN26_c1_g3_i2 lend:2492 rend:2771 [103000 lines read] scaff:TRINITY_DN26_c1_g3_i2 lend:4155 rend:4362 [104000 lines read] scaff:TRINITY_DN26_c1_g3_i2 lend:5546 rend:5852 [105000 lines read] scaff:TRINITY_DN26_c1_g3_i3 lend:1418 rend:1631 [106000 lines read] scaff:TRINITY_DN26_c1_g3_i4 lend:312 rend:579 [107000 lines read] scaff:TRINITY_DN26_c1_g3_i4 lend:2113 rend:2396 [108000 lines read] scaff:TRINITY_DN26_c1_g3_i4 lend:3741 rend:3970 [109000 lines read] scaff:TRINITY_DN26_c1_g3_i4 lend:5312 rend:5790 [110000 lines read] scaff:TRINITY_DN26_c1_g3_i5 lend:959 rend:1186 [111000 lines read] scaff:TRINITY_DN26_c1_g3_i5 lend:2690 rend:3027 [112000 lines read] scaff:TRINITY_DN26_c2_g1_i1 lend:2009 rend:2303 [113000 lines read] scaff:TRINITY_DN26_c2_g1_i1 lend:5214 rend:5424 [114000 lines read] scaff:TRINITY_DN26_c2_g1_i1 lend:7232 rend:7518 [115000 lines read] scaff:TRINITY_DN26_c2_g1_i1 lend:8563 rend:8806 [116000 lines read] scaff:TRINITY_DN26_c2_g1_i3 lend:3594 rend:3804 [117000 lines read] scaff:TRINITY_DN26_c2_g1_i3 lend:6104 rend:6308 [118000 lines read] scaff:TRINITY_DN26_c2_g1_i3 lend:7756 rend:8174 [119000 lines read] scaff:TRINITY_DN26_c2_g1_i4 lend:1469 rend:1695 [120000 lines read] scaff:TRINITY_DN26_c2_g1_i4 lend:4612 rend:4930 [121000 lines read] scaff:TRINITY_DN26_c2_g1_i5 lend:319 rend:619 [122000 lines read] scaff:TRINITY_DN26_c2_g1_i5 lend:4182 rend:4550 [123000 lines read] scaff:TRINITY_DN26_c2_g1_i5 lend:6476 rend:6807 [124000 lines read] scaff:TRINITY_DN26_c2_g1_i5 lend:8272 rend:8467 CMD: touch transAligns.cSorted.bam.norm_200.bam.frag_coverage.wig.ok 1928s CMD: /usr/lib/trinityrnaseq/util/support_scripts/define_coverage_partitions.pl transAligns.cSorted.bam.norm_200.bam.frag_coverage.wig 1 + > transAligns.cSorted.bam.norm_200.bam.minC1.gff 1929s CMD: touch transAligns.cSorted.bam.norm_200.bam.minC1.gff.ok 1929s CMD: /usr/lib/trinityrnaseq/util/support_scripts/extract_reads_per_partition.pl --partitions_gff transAligns.cSorted.bam.norm_200.bam.minC1.gff --coord_sorted_SAM transAligns.cSorted.bam.norm_200.bam --parts_per_directory 100 --min_reads_per_partition 10 1929s // parsing paritions. 1929s [92] -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN0_c0_g1_i1/0/1_251.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN10_c0_g1_i1/0/1_307.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN12_c0_g1_i1/0/1_246.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN12_c0_g1_i2/0/1_312.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN14_c0_g1_i1/0/1_280.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN14_c0_g2_i1/0/1_390.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN15_c0_g1_i1/0/1_239.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN16_c0_g1_i1/0/1_272.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN16_c0_g2_i1/0/1_324.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN18_c0_g1_i1/0/36_344.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN18_c0_g1_i2/0/36_348.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN19_c0_g1_i1/0/1_304.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i1/0/1_769.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g2_i1/0/1_484.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i2/0/3_2306.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i3/0/1_2226.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i4/0/1_2619.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i5/0/1_1442.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i6/0/1_1946.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i7/0/1_2899.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN21_c0_g1_i1/0/1_2802.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN21_c0_g1_i2/0/1_3823.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g1_i1/0/1_422.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g2_i1/0/1_204.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i1/0/1_2433.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g4_i1/0/1_219.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i2/0/1_790.trinity.reads 1929s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i3/0/1_2269.trinity.reads 1930s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i4/0/1_2200.trinity.reads 1930s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g5_i1/0/1_590.trinity.reads 1930s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g6_i1/0/1_246.trinity.reads 1930s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i5/0/1_2364.trinity.reads 1930s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g7_i1/0/1_513.trinity.reads 1930s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i1/0/1_799.trinity.reads 1930s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g2_i1/0/1_205.trinity.reads 1930s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i2/0/1_2592.trinity.reads 1930s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g3_i1/0/1_289.trinity.reads 1930s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g4_i1/0/1_341.trinity.reads 1930s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g5_i1/0/1_952.trinity.reads 1930s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i3/0/1_2514.trinity.reads 1930s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i4/0/1_296.trinity.reads 1930s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g1_i1/0/1_205.trinity.reads 1930s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g2_i1/0/1_433.trinity.reads 1930s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g3_i1/0/3_7194.trinity.reads 1931s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g3_i2/0/2_530.trinity.reads 1931s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i1/0/1_1375.trinity.reads 1931s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i2/0/1_3516.trinity.reads 1931s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i3/0/1_3667.trinity.reads 1931s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i4/0/1_3625.trinity.reads 1932s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i5/0/1_220.trinity.reads 1932s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c0_g1_i1/0/1_5399.trinity.reads 1932s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c0_g1_i2/0/1_5528.trinity.reads 1932s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i1/0/1_8158.trinity.reads 1932s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i2/0/1_8134.trinity.reads 1932s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i3/0/1_8130.trinity.reads 1933s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i4/0/1_8138.trinity.reads 1933s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i5/0/1_8087.trinity.reads 1933s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i6/0/1_8146.trinity.reads 1933s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g2_i1/0/1_341.trinity.reads 1933s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i7/0/1_8091.trinity.reads 1933s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i1/0/1_5713.trinity.reads 1934s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i8/0/1_8079.trinity.reads 1934s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i9/0/1_8122.trinity.reads 1934s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i10/0/1_8150.trinity.reads 1934s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i11/0/1_6104.trinity.reads 1934s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i2/0/1_5905.trinity.reads 1935s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i12/0/1_8130.trinity.reads 1935s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g4_i1/0/1_298.trinity.reads 1935s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i13/0/1_8126.trinity.reads 1935s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i14/0/1_8091.trinity.reads 1935s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i15/0/1_8095.trinity.reads 1935s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i16/0/1_8150.trinity.reads 1935s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i17/0/1_8142.trinity.reads 1936s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i18/0/1_8099.trinity.reads 1936s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i3/0/1_3101.trinity.reads 1936s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i19/0/1_6546.trinity.reads 1936s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i4/0/1_5854.trinity.reads 1936s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g5_i1/0/1_215.trinity.reads 1936s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i20/0/1_8154.trinity.reads 1937s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i21/0/1_6129.trinity.reads 1937s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i5/0/1_3918.trinity.reads 1937s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i1/0/1_8817.trinity.reads 1937s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i2/0/44_633.trinity.reads 1937s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g2_i1/0/1_281.trinity.reads 1937s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g3_i1/0/1_491.trinity.reads 1937s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i3/0/1_8757.trinity.reads 1937s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i4/0/1_6795.trinity.reads 1938s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i5/0/1_8973.trinity.reads 1938s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN27_c0_g1_i1/0/1_261.trinity.reads 1938s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN4_c0_g1_i1/0/1_329.trinity.reads 1938s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN5_c0_g1_i1/0/1_252.trinity.reads 1938s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN7_c0_g1_i1/0/1_301.trinity.reads 1938s CMD: touch Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff.ok 1938s ## 1938s Done 1938s ## 1938s 1938s Saturday, November 2, 2024: 18:09:14 CMD: touch partitions.ok 1938s Saturday, November 2, 2024: 18:09:14 CMD: find Dir_* -name '*reads' > read_files.list 1938s Saturday, November 2, 2024: 18:09:14 CMD: touch read_files.list.ok 1938s Saturday, November 2, 2024: 18:09:14 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file read_files.list --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --full_cleanup > trinity_GG.cmds 1938s Saturday, November 2, 2024: 18:09:14 CMD: touch trinity_GG.cmds.ok 1938s Saturday, November 2, 2024: 18:09:14 CMD: touch trinity_GG.cmds.ok 1938s 1938s 1938s -------------------------------------------------------------------------------- 1938s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 1938s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 1938s -------------------------------------------------------------------------------- 1938s 1938s Saturday, November 2, 2024: 18:09:14 CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -v -shuffle 1938s Number of Commands: 85 2229s succeeded(1) 1.17647% completed. succeeded(2) 2.35294% completed. succeeded(3) 3.52941% completed. succeeded(4) 4.70588% completed. succeeded(5) 5.88235% completed. succeeded(6) 7.05882% completed. succeeded(7) 8.23529% completed. succeeded(8) 9.41177% completed. succeeded(9) 10.5882% completed. succeeded(10) 11.7647% completed. succeeded(11) 12.9412% completed. succeeded(12) 14.1176% completed. succeeded(13) 15.2941% completed. succeeded(14) 16.4706% completed. succeeded(15) 17.6471% completed. succeeded(16) 18.8235% completed. succeeded(17) 20% completed. succeeded(18) 21.1765% completed. succeeded(19) 22.3529% completed. succeeded(20) 23.5294% completed. succeeded(21) 24.7059% completed. succeeded(22) 25.8824% completed. succeeded(23) 27.0588% completed. succeeded(24) 28.2353% completed. succeeded(25) 29.4118% completed. succeeded(26) 30.5882% completed. succeeded(27) 31.7647% completed. succeeded(28) 32.9412% completed. succeeded(29) 34.1176% completed. succeeded(30) 35.2941% completed. succeeded(31) 36.4706% completed. succeeded(32) 37.6471% completed. succeeded(33) 38.8235% completed. succeeded(34) 40% completed. succeeded(35) 41.1765% completed. succeeded(36) 42.3529% completed. succeeded(37) 43.5294% completed. succeeded(38) 44.7059% completed. succeeded(39) 45.8824% completed. succeeded(40) 47.0588% completed. succeeded(41) 48.2353% completed. succeeded(42) 49.4118% completed. succeeded(43) 50.5882% completed. succeeded(44) 51.7647% completed. succeeded(45) 52.9412% completed. succeeded(46) 54.1176% completed. succeeded(47) 55.2941% completed. succeeded(48) 56.4706% completed. succeeded(49) 57.6471% completed. succeeded(50) 58.8235% completed. succeeded(51) 60% completed. succeeded(52) 61.1765% completed. succeeded(53) 62.3529% completed. succeeded(54) 63.5294% completed. succeeded(55) 64.7059% completed. succeeded(56) 65.8824% completed. succeeded(57) 67.0588% completed. succeeded(58) 68.2353% completed. succeeded(59) 69.4118% completed. succeeded(60) 70.5882% completed. succeeded(61) 71.7647% completed. succeeded(62) 72.9412% completed. succeeded(63) 74.1176% completed. succeeded(64) 75.2941% completed. succeeded(65) 76.4706% completed. succeeded(66) 77.6471% completed. succeeded(67) 78.8235% completed. succeeded(68) 80% completed. succeeded(69) 81.1765% completed. succeeded(70) 82.3529% completed. succeeded(71) 83.5294% completed. succeeded(72) 84.7059% completed. succeeded(73) 85.8824% completed. succeeded(74) 87.0588% completed. succeeded(75) 88.2353% completed. succeeded(76) 89.4118% completed. succeeded(77) 90.5882% completed. succeeded(78) 91.7647% completed. succeeded(79) 92.9412% completed. succeeded(80) 94.1176% completed. succeeded(81) 95.2941% completed. succeeded(82) 96.4706% completed. succeeded(83) 97.6471% completed. succeeded(84) 98.8235% completed. succeeded(85) 100% completed. 2229s 2229s All commands completed successfully. :-) 2229s 2229s Saturday, November 2, 2024: 18:14:05 CMD: find Dir_* -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta.tmp 2229s Saturday, November 2, 2024: 18:14:05 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta.gene_trans_map 2229s 2229s 2229s Finished. See /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta for reconstructed transcripts 2229s 2229s 2229s 2229s outfile="test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta" 2229s asmsize=$(wc -c <"${outfile}") 2229s if [ $asmsize -le 650000 ]; then 2229s echo "Error, ${outfile} potentially incomplete" 2229s exit 1 2229s else 2229s echo "ok" 2229s exit 0 2229s fi 2229s ok 2229s ./run_chr17_GG_wLongreads.sh 2229s #!/bin/bash -ve 2229s 2229s 2229s $TRINITY_HOME/Trinity --genome_guided_max_intron 100000 --genome_guided_bam chr17.illumina.bam --long_reads_bam chr17.pbio.bam --max_memory 2G --output test_chr17_LR_GG_trinity_outdir --CPU 5 --no_cleanup 2229s 2229s 2229s ______ ____ ____ ____ ____ ______ __ __ 2229s | || \ | || \ | || || | | 2229s | || D ) | | | _ | | | | || | | 2229s |_| |_|| / | | | | | | | |_| |_|| ~ | 2229s | | | \ | | | | | | | | | |___, | 2229s | | | . \ | | | | | | | | | | | 2229s |__| |__|\_||____||__|__||____| |__| |____/ 2229s 2229s Trinity-v2.15.1 2229s 2229s 2229s 2229s Saturday, November 2, 2024: 18:14:05 CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl chr17.illumina.bam 2229s -appears to be a coordinate sorted bam file. ok. 2229s Saturday, November 2, 2024: 18:14:05 CMD: mkdir -p /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir 2229s 2229s 2229s ---------------------------------------------------------------------------------- 2229s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- 2229s ---------------------------------------------------------------------------------- 2229s 2229s -found paired-end aligned read. Running in paired-end mode. 2229s Saturday, November 2, 2024: 18:14:05 CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.illumina.bam.norm_200.bam --keep_secondary /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.illumina.bam 2230s Done with chr chr1. 2230s Saturday, November 2, 2024: 18:14:06 CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.illumina.bam.norm_200.bam.ok 2230s * [Sat Nov 2 18:14:06 2024] Running CMD: java -jar /usr/share/java/picard.jar AddOrReplaceReadGroups I=/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam O=/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.pbio.bam.RGLR.bam RGID=PBLR RGLB=lib2 RGPL=pacbio RGPU=unit2 RGSM=pacbio VALIDATION_STRINGENCY=LENIENT 2232s INFO 2024-11-02 18:14:08 AddOrReplaceReadGroups 2232s 2232s ********** NOTE: Picard's command line syntax is changing. 2232s ********** 2232s ********** For more information, please see: 2232s ********** 2232s https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) 2232s ********** 2232s ********** The command line looks like this in the new syntax: 2232s ********** 2232s ********** AddOrReplaceReadGroups -I /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam -O /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.pbio.bam.RGLR.bam -RGID PBLR -RGLB lib2 -RGPL pacbio -RGPU unit2 -RGSM pacbio -VALIDATION_STRINGENCY LENIENT 2232s ********** 2232s 2232s 2232s 18:14:08.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 2232s 18:14:08.249 WARN NativeLibraryLoader - LD_LIBRARY_PATH = :/usr/lib/trinityrnaseq/trinity-plugins/htslib 2232s 18:14:08.250 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 2232s 18:14:08.252 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 2232s 18:14:08.252 WARN NativeLibraryLoader - LD_LIBRARY_PATH = :/usr/lib/trinityrnaseq/trinity-plugins/htslib 2232s 18:14:08.252 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 2232s [Sat Nov 02 18:14:08 UTC 2024] AddOrReplaceReadGroups INPUT=/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam OUTPUT=/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.pbio.bam.RGLR.bam RGID=PBLR RGLB=lib2 RGPL=pacbio RGPU=unit2 RGSM=pacbio VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false 2232s [Sat Nov 02 18:14:08 UTC 2024] Executing as ubuntu@autopkgtest on Linux 6.11.0-8-generic amd64; OpenJDK 64-Bit Server VM 21.0.5+11-Ubuntu-1; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: 3.1.1 2232s 18:14:08.275 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater 2232s 18:14:08.287 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater 2232s INFO 2024-11-02 18:14:08 AddOrReplaceReadGroups Created read-group ID=PBLR PL=pacbio LB=lib2 SM=pacbio 2232s 2232s 18:14:08.346 WARN IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater 2232s [Sat Nov 02 18:14:08 UTC 2024] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.01 minutes. 2232s Runtime.totalMemory()=67108864 2232s * [Sat Nov 2 18:14:08 2024] Running CMD: samtools merge /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.illumina.bam.norm_200.bam /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.pbio.bam.RGLR.bam && samtools index /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam 2233s Saturday, November 2, 2024: 18:14:09 CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam -I 100000 --sort_buffer 2G --CPU 5 2233s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --CPU 5 --sort_buffer 2G --sam merged_wRGLR.bam --min_insert_size 1 --max_insert_size 100000 2233s -extracting read coordinates from merged_wRGLR.bam into merged_wRGLR.bam.read_coords 2233s 2236s CMD: touch merged_wRGLR.bam.read_coords.ok 2236s CMD: /usr/bin/sort --parallel=5 -S2G -T . -k1,1 -k2,2 -k4,4n merged_wRGLR.bam.read_coords > merged_wRGLR.bam.read_coords.sort_by_readname 2236s CMD: cp /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam.read_coords /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam.read_coords.sort_by_readname 2236s CMD: /usr/bin/sort --parallel=5 -S2G -T . -k1,1 -k3,3n merged_wRGLR.bam.frag_coords > merged_wRGLR.bam.frag_coords.coord_sorted 2236s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl merged_wRGLR.bam.frag_coords > merged_wRGLR.bam.frag_coverage.wig 2256s [1000 lines read] scaff:chr17 lend:441683 rend:441971 [2000 lines read] scaff:chr17 lend:745759 rend:746264 [3000 lines read] scaff:chr17 lend:770696 rend:770752 [4000 lines read] scaff:chr17 lend:1344888 rend:1345193 [5000 lines read] scaff:chr17 lend:1420877 rend:1421141 [6000 lines read] scaff:chr17 lend:1464472 rend:1465037 [7000 lines read] scaff:chr17 lend:1519178 rend:1519476 [8000 lines read] scaff:chr17 lend:1646492 rend:1647958 [9000 lines read] scaff:chr17 lend:1653900 rend:1658553 [10000 lines read] scaff:chr17 lend:1660471 rend:1660818 [11000 lines read] scaff:chr17 lend:1675653 rend:1676697 [12000 lines read] scaff:chr17 lend:1681518 rend:1681972 [13000 lines read] scaff:chr17 lend:1776582 rend:1777325 [14000 lines read] scaff:chr17 lend:1879302 rend:1891925 [15000 lines read] scaff:chr17 lend:2042921 rend:2043283 [16000 lines read] scaff:chr17 lend:2322233 rend:2322871 [17000 lines read] scaff:chr17 lend:2325416 rend:2331108 [18000 lines read] scaff:chr17 lend:2377747 rend:2379616 [19000 lines read] scaff:chr17 lend:2486702 rend:2487026 [20000 lines read] scaff:chr17 lend:2682083 rend:2682640 [21000 lines read] scaff:chr17 lend:2689842 rend:2690324 [22000 lines read] scaff:chr17 lend:2698334 rend:2701265 [23000 lines read] scaff:chr17 lend:3663158 rend:3664210 [24000 lines read] scaff:chr17 lend:3811005 rend:3811630 [25000 lines read] scaff:chr17 lend:3894240 rend:3894816 [26000 lines read] scaff:chr17 lend:3926179 rend:3926793 [27000 lines read] scaff:chr17 lend:4009633 rend:4016371 [28000 lines read] scaff:chr17 lend:4165239 rend:4165812 [29000 lines read] scaff:chr17 lend:4260001 rend:4263956 [30000 lines read] scaff:chr17 lend:4289368 rend:4366449 [31000 lines read] scaff:chr17 lend:4552617 rend:4555359 [32000 lines read] scaff:chr17 lend:4717232 rend:4720296 [33000 lines read] scaff:chr17 lend:4892199 rend:4893532 [34000 lines read] scaff:chr17 lend:4940095 rend:4940710 [35000 lines read] scaff:chr17 lend:4946801 rend:4948447 [36000 lines read] scaff:chr17 lend:4982444 rend:4986216 CMD: touch merged_wRGLR.bam.frag_coverage.wig.ok 2256s CMD: /usr/lib/trinityrnaseq/util/support_scripts/define_coverage_partitions.pl merged_wRGLR.bam.frag_coverage.wig 1 + > merged_wRGLR.bam.minC1.gff 2261s CMD: touch merged_wRGLR.bam.minC1.gff.ok 2261s CMD: /usr/lib/trinityrnaseq/util/support_scripts/extract_reads_per_partition.pl --partitions_gff merged_wRGLR.bam.minC1.gff --coord_sorted_SAM merged_wRGLR.bam --parts_per_directory 100 --min_reads_per_partition 10 2261s // parsing paritions. 2261s [100] [116] -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/60324_60754.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/60950_61267.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/61474_118580.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/205351_205672.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/210418_210982.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/213769_219690.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/229120_229684.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/263847_264260.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/270652_271297.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/281768_441038.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/441045_445940.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/511494_511801.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/512042_512389.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/512759_514091.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/514571_714865.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/714910_715353.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/715370_716236.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/716302_716978.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/717455_718543.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/718787_719490.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/719569_720181.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/720720_721596.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/721666_722031.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/726239_726536.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/729712_730684.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/730918_731668.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/731742_732126.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/732418_752287.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/752375_752769.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/753167_754706.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/758974_782331.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/782362_792510.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/793543_794109.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/795176_795754.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/799707_800316.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/800915_803792.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/981902_982655.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/997125_1091796.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1146722_1146846.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1148302_1149226.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1151011_1152011.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1153293_1153810.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1226770_1227467.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1257967_1400270.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1414443_1415081.trinity.reads 2261s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1420724_2022954.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2030147_2043980.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2044654_2045225.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2047917_2048512.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2049091_2049553.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2051694_2052378.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2053479_2053635.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2054237_2054372.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2054544_2056751.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2056812_2057391.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2058177_2058912.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2059847_2303836.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2303955_2336468.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2336627_2337019.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2337198_2381047.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2384152_2401123.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2401365_2401725.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2404365_2404707.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2405573_2732999.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2956146_2956563.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2975679_2985002.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2991366_3008124.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3020537_3033568.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3033777_3034364.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3035321_3035959.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3036150_3036658.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3267590_3274822.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3328495_3331689.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3421757_3422307.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3422776_3423370.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3440227_3513828.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3565576_3566168.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3566800_3572235.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3573782_3585901.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3586814_3587176.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3589817_3592166.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3592533_3592851.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3605115_3605237.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3606109_3607928.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3607968_3636272.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3636486_3668698.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3668798_3670060.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3670078_3670807.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3673537_3681945.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3689987_3695886.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3706252_3917856.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3923874_3964467.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3964821_3965192.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4001444_4001952.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4003050_4003706.trinity.reads 2262s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4004424_4555389.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4660854_4661151.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4667839_4668289.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4671192_4704136.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4704234_4705420.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4710502_4721496.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4731419_4733592.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4734646_4739376.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4787354_4789638.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4796155_4798495.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4805950_4806545.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4807192_4823373.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4833366_4897982.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4904417_4904897.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4927248_4928577.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4928729_4928949.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4929025_4934979.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4935086_4935300.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4935439_4945214.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4945652_4997520.trinity.reads 2263s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4997681_5001302.trinity.reads 2263s CMD: touch Dir_merged_wRGLR.bam.minC1.gff.ok 2263s ## 2263s Done 2263s ## 2263s 2263s Saturday, November 2, 2024: 18:14:39 CMD: touch partitions.ok 2263s Saturday, November 2, 2024: 18:14:39 CMD: find Dir_* -name '*reads' > read_files.list 2263s Saturday, November 2, 2024: 18:14:39 CMD: touch read_files.list.ok 2263s Saturday, November 2, 2024: 18:14:39 CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file read_files.list --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --no_cleanup --long_reads_mode > trinity_GG.cmds 2263s Saturday, November 2, 2024: 18:14:39 CMD: touch trinity_GG.cmds.ok 2263s Saturday, November 2, 2024: 18:14:39 CMD: touch trinity_GG.cmds.ok 2263s 2263s 2263s -------------------------------------------------------------------------------- 2263s ------------ Trinity Phase 2: Assembling Clusters of Reads --------------------- 2263s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) --------------- 2263s -------------------------------------------------------------------------------- 2263s 2263s Saturday, November 2, 2024: 18:14:39 CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 5 -v -shuffle 2263s Number of Commands: 44 2875s succeeded(1) 2.27273% completed. succeeded(2) 4.54545% completed. succeeded(3) 6.81818% completed. succeeded(4) 9.09091% completed. succeeded(5) 11.3636% completed. succeeded(6) 13.6364% completed. succeeded(7) 15.9091% completed. succeeded(8) 18.1818% completed. succeeded(9) 20.4545% completed. succeeded(10) 22.7273% completed. succeeded(11) 25% completed. succeeded(12) 27.2727% completed. succeeded(13) 29.5455% completed. succeeded(14) 31.8182% completed. succeeded(15) 34.0909% completed. succeeded(16) 36.3636% completed. succeeded(17) 38.6364% completed. succeeded(18) 40.9091% completed. succeeded(19) 43.1818% completed. succeeded(20) 45.4545% completed. succeeded(21) 47.7273% completed. succeeded(22) 50% completed. succeeded(23) 52.2727% completed. succeeded(24) 54.5455% completed. succeeded(25) 56.8182% completed. succeeded(26) 59.0909% completed. succeeded(27) 61.3636% completed. succeeded(28) 63.6364% completed. succeeded(29) 65.9091% completed. succeeded(30) 68.1818% completed. succeeded(31) 70.4545% completed. succeeded(32) 72.7273% completed. succeeded(33) 75% completed. succeeded(34) 77.2727% completed. succeeded(35) 79.5455% completed. succeeded(36) 81.8182% completed. succeeded(37) 84.0909% completed. succeeded(38) 86.3636% completed. succeeded(39) 88.6364% completed. succeeded(40) 90.9091% completed. succeeded(41) 93.1818% completed. succeeded(42) 95.4545% completed. succeeded(43) 97.7273% completed. succeeded(44) 100% completed. 2875s 2875s All commands completed successfully. :-) 2875s 2875s Saturday, November 2, 2024: 18:24:51 CMD: find Dir_* -name '*inity.fasta' | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta.tmp 2875s Saturday, November 2, 2024: 18:24:51 CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta.gene_trans_map 2875s 2875s 2875s Finished. See /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta for reconstructed transcripts 2875s 2875s 2875s find test_chr17_LR_GG_trinity_outdir/ -regex ".*allProbPaths.fasta" -exec cat {} \; | grep '>' | grep 'LR\$' > test_chr17_LR_GG_trinity_outdir.LR 2876s 2876s if [[ $(wc -l > left.fa 2876s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz) >> right.fa 2876s CMD finished (0 seconds) 2876s CMD finished (0 seconds) 2876s CMD: touch left.fa.ok 2876s CMD finished (0 seconds) 2876s CMD: touch right.fa.ok 2876s CMD finished (0 seconds) 2876s Done converting input files.CMD: cat left.fa right.fa > both.fa 2876s CMD finished (0 seconds) 2876s CMD: touch both.fa.ok 2876s CMD finished (0 seconds) 2876s -kmer counting. 2876s ------------------------------------------- 2876s ----------- Jellyfish -------------------- 2876s -- (building a k-mer catalog from reads) -- 2876s ------------------------------------------- 2876s 2876s CMD: jellyfish count -t 2 -m 25 -s 100000000 --canonical both.fa 2878s CMD finished (2 seconds) 2878s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 2878s CMD finished (0 seconds) 2878s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 2878s CMD finished (0 seconds) 2878s CMD: touch jellyfish.K25.min2.kmers.fa.success 2878s CMD finished (0 seconds) 2878s -generating stats files 2878s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 2 --DS > left.fa.K25.stats 2878s -reading Kmer occurrences... 2878s 2878s done parsing 100964 Kmers, 100964 added, taking 0 seconds. 2878s STATS_GENERATION_TIME: 0 seconds. 2878s CMD finished (0 seconds) 2878s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 2 --DS > right.fa.K25.stats 2878s -reading Kmer occurrences... 2879s 2879s done parsing 100964 Kmers, 100964 added, taking 1 seconds. 2879s STATS_GENERATION_TIME: 0 seconds. 2879s CMD finished (1 seconds) 2879s CMD: touch left.fa.K25.stats.ok 2879s CMD finished (0 seconds) 2879s CMD: touch right.fa.K25.stats.ok 2879s CMD finished (0 seconds) 2879s -sorting each stats file by read name. 2879s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 2G >> left.fa.K25.stats.sort 2879s CMD finished (0 seconds) 2879s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 2G >> right.fa.K25.stats.sort 2879s CMD finished (0 seconds) 2879s CMD: touch left.fa.K25.stats.sort.ok 2879s CMD finished (0 seconds) 2879s CMD: touch right.fa.K25.stats.sort.ok 2879s CMD finished (0 seconds) 2879s -defining normalized reads 2879s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats 2879s -opening left.fa.K25.stats.sort 2879s -opening right.fa.K25.stats.sort 2879s -done opening files. 2880s CMD finished (1 seconds) 2880s CMD: touch pairs.K25.stats.ok 2880s CMD finished (0 seconds) 2880s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 5 --min_cov 2 --max_CV 10000 > pairs.K25.stats.C5.maxCV10000.accs 2880s 3826 / 30575 = 12.51% reads selected during normalization. 2880s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles. 2880s 1797 / 30575 = 5.88% reads discarded as below minimum coverage threshold=2 2880s CMD finished (0 seconds) 2880s CMD: touch pairs.K25.stats.C5.maxCV10000.accs.ok 2880s CMD finished (0 seconds) 2880s -search and capture. 2880s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz ... done prepping, now search and capture. 2880s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz 2880s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz ... done prepping, now search and capture. 2880s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz 2880s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.left.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq.ok 2880s CMD finished (0 seconds) 2880s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.right.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq.ok 2880s CMD finished (0 seconds) 2880s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.left.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq left.norm.fq 2880s CMD finished (0 seconds) 2880s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.right.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq right.norm.fq 2880s CMD finished (0 seconds) 2880s 2880s 2880s Normalization complete. See outputs: 2880s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.left.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq 2880s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.right.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq 2880s 2880s 2880s 2880s ./test_SE_normalization.sh 2880s #!/bin/bash -ve 2880s 2880s if [ ! -e reads.single.fq ]; then 2880s gunzip -c ../test_DATA/reads.left.fq.gz > reads.single.fq 2880s fi 2880s 2880s 2880s # just for testing purposes, use --max_cov 30 or higher for real applications. 2880s $TRINITY_HOME/util/insilico_read_normalization.pl --JM 2G --single reads.single.fq --seqType fq --max_cov 5 --no_cleanup --tmp_dir_name single_tmp_norm_reads 2880s -prepping seqs 2880s CMD: seqtk-trinity seq -A -R 1 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq >> single.fa 2880s CMD finished (0 seconds) 2880s CMD: touch single.fa.ok 2880s CMD finished (0 seconds) 2880s -kmer counting. 2880s ------------------------------------------- 2880s ----------- Jellyfish -------------------- 2880s -- (building a k-mer catalog from reads) -- 2880s ------------------------------------------- 2880s 2880s CMD: jellyfish count -t 2 -m 25 -s 100000000 --canonical single.fa 2882s CMD finished (1 seconds) 2882s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 2882s CMD finished (0 seconds) 2882s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 2882s CMD finished (0 seconds) 2882s CMD: touch jellyfish.K25.min2.kmers.fa.success 2882s CMD finished (0 seconds) 2882s -generating stats files 2882s CMD: /usr/bin/fastaToKmerCoverageStats --reads single.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 2 --DS > single.fa.K25.stats 2882s -reading Kmer occurrences... 2882s 2882s done parsing 70076 Kmers, 70076 added, taking 0 seconds. 2883s STATS_GENERATION_TIME: 1 seconds. 2883s CMD finished (1 seconds) 2883s CMD: touch single.fa.K25.stats.ok 2883s CMD finished (0 seconds) 2883s -sorting each stats file by read name. 2883s CMD: head -n1 single.fa.K25.stats > single.fa.K25.stats.sort && tail -n +2 single.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 2G >> single.fa.K25.stats.sort 2883s CMD finished (0 seconds) 2883s CMD: touch single.fa.K25.stats.sort.ok 2883s CMD finished (0 seconds) 2883s -defining normalized reads 2883s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file single.fa.K25.stats.sort --max_cov 5 --min_cov 0 --max_CV 10000 > single.fa.K25.stats.sort.maxC5.minC0.maxCV10000.accs 2883s 9127 / 30575 = 29.85% reads selected during normalization. 2883s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles. 2883s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=0 2883s CMD finished (0 seconds) 2883s CMD: touch single.fa.K25.stats.sort.maxC5.minC0.maxCV10000.accs.ok 2883s CMD finished (0 seconds) 2883s -search and capture. 2883s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq ... done prepping, now search and capture. 2883s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq 2883s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq.normalized_K25_maxC5_minC0_maxCV10000.fq.ok 2883s CMD finished (0 seconds) 2883s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq.normalized_K25_maxC5_minC0_maxCV10000.fq single.norm.fq 2883s CMD finished (0 seconds) 2883s 2883s 2883s Normalization complete. See outputs: 2883s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq.normalized_K25_maxC5_minC0_maxCV10000.fq 2883s 2883s 2883s 2883s ./test_PE_normalization.mult_read_sets.sh 2883s #!/bin/bash -ve 2883s 2883s CPU=$(nproc || sysctl -n hw.physicalcpu) 2883s 2883s # just for testing purposes, use --max_cov 30 or higher for real applications. 2883s $TRINITY_HOME/util/insilico_read_normalization.pl --JM 2G \ 2883s --left ../test_DATA/reads.left.fq.gz,../test_DATA/reads2.left.fq.gz \ 2883s --right ../test_DATA/reads.right.fq.gz,../test_DATA/reads2.right.fq.gz \ 2883s --seqType fq --max_cov 5 --pairs_together --no_cleanup --CPU ${CPU} --tmp_dir_name tmp_PE_mult_norm_dir \ 2883s --output test_multi_read_sets_norm_outdir 2883s -prepping seqs 2883s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz) >> left.fa 2883s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz) >> right.fa 2884s CMD finished (1 seconds) 2884s CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.right.fq.gz) >> right.fa 2884s CMD finished (1 seconds) 2884s CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.left.fq.gz) >> left.fa 2884s CMD finished (0 seconds) 2884s CMD finished (0 seconds) 2884s CMD: touch left.fa.ok 2884s CMD finished (0 seconds) 2884s CMD: touch right.fa.ok 2884s CMD finished (0 seconds) 2884s Done converting input files.CMD: cat left.fa right.fa > both.fa 2884s CMD finished (0 seconds) 2884s CMD: touch both.fa.ok 2884s CMD finished (0 seconds) 2884s -kmer counting. 2884s ------------------------------------------- 2884s ----------- Jellyfish -------------------- 2884s -- (building a k-mer catalog from reads) -- 2884s ------------------------------------------- 2884s 2884s CMD: jellyfish count -t 2 -m 25 -s 100000000 --canonical both.fa 2886s CMD finished (2 seconds) 2886s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf 2886s CMD finished (0 seconds) 2886s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa 2886s CMD finished (0 seconds) 2886s CMD: touch jellyfish.K25.min2.kmers.fa.success 2886s CMD finished (0 seconds) 2886s -generating stats files 2886s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 2 --DS > left.fa.K25.stats 2886s -reading Kmer occurrences... 2886s 2886s done parsing 518514 Kmers, 518514 added, taking 0 seconds. 2887s STATS_GENERATION_TIME: 1 seconds. 2887s CMD finished (1 seconds) 2887s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 2 --DS > right.fa.K25.stats 2887s -reading Kmer occurrences... 2888s 2888s done parsing 518514 Kmers, 518514 added, taking 1 seconds. 2889s STATS_GENERATION_TIME: 1 seconds. 2889s CMD finished (2 seconds) 2889s CMD: touch left.fa.K25.stats.ok 2889s CMD finished (0 seconds) 2889s CMD: touch right.fa.K25.stats.ok 2889s CMD finished (0 seconds) 2889s -sorting each stats file by read name. 2889s CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 2G >> left.fa.K25.stats.sort 2889s CMD finished (0 seconds) 2889s CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 2G >> right.fa.K25.stats.sort 2889s CMD finished (0 seconds) 2889s CMD: touch left.fa.K25.stats.sort.ok 2889s CMD finished (0 seconds) 2889s CMD: touch right.fa.K25.stats.sort.ok 2889s CMD finished (0 seconds) 2889s -defining normalized reads 2889s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats 2889s -opening left.fa.K25.stats.sort 2889s -opening right.fa.K25.stats.sort 2889s -done opening files. 2890s CMD finished (1 seconds) 2890s CMD: touch pairs.K25.stats.ok 2890s CMD finished (0 seconds) 2890s CMD: /usr/lib/trinityrnaseq//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 5 --min_cov 0 --max_CV 10000 > pairs.K25.stats.C5.maxCV10000.accs 2891s 7970 / 61150 = 13.03% reads selected during normalization. 2891s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles. 2891s 0 / 61150 = 0.00% reads discarded as below minimum coverage threshold=0 2891s CMD finished (1 seconds) 2891s CMD: touch pairs.K25.stats.C5.maxCV10000.accs.ok 2891s CMD finished (0 seconds) 2891s -search and capture. 2891s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.left.fq.gz ... done prepping, now search and capture. 2891s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz 2891s -preparing to extract selected reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.right.fq.gz ... done prepping, now search and capture. 2891s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz 2891s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.left.fq.gz 2891s -capturing normalized reads from: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.right.fq.gz 2892s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/test_multi_read_sets_norm_outdir/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC5_minC0_maxCV10000.fq.ok 2892s CMD finished (0 seconds) 2892s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/test_multi_read_sets_norm_outdir/reads.right.fq.gz_ext_all_reads.normalized_K25_maxC5_minC0_maxCV10000.fq.ok 2892s CMD finished (0 seconds) 2892s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/test_multi_read_sets_norm_outdir/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC5_minC0_maxCV10000.fq left.norm.fq 2892s CMD finished (0 seconds) 2892s CMD: ln -sf /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/test_multi_read_sets_norm_outdir/reads.right.fq.gz_ext_all_reads.normalized_K25_maxC5_minC0_maxCV10000.fq right.norm.fq 2892s CMD finished (0 seconds) 2892s 2892s 2892s Normalization complete. See outputs: 2892s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/test_multi_read_sets_norm_outdir/reads.left.fq.gz_ext_all_reads.normalized_K25_maxC5_minC0_maxCV10000.fq 2892s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/test_multi_read_sets_norm_outdir/reads.right.fq.gz_ext_all_reads.normalized_K25_maxC5_minC0_maxCV10000.fq 2892s 2892s 2892s 2892s touch test 2892s make[1]: Leaving directory '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization' 2892s Running example in test_DE_analysis... 2892s make[1]: Entering directory '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis' 2892s Running example in Candida_example... 2892s make[2]: Entering directory '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example' 2892s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method edgeR -s samples.txt -o edgeR_outdir 2892s Got 9 samples, and got: 10 data fields. 2892s Header: wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 2892s Next: TR24|c0_g1_i1 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00 2892s 2892s $VAR1 = { 2892s 'wt_GSNO_3' => 4, 2892s 'wt_GSNO_2' => 6, 2892s 'wt_ph8_2' => 9, 2892s 'wt_37_3' => 2, 2892s 'wt_ph8_1' => 8, 2892s 'wt_37_2' => 1, 2892s 'wt_ph8_3' => 7, 2892s 'wt_GSNO_1' => 5, 2892s 'wt_37_1' => 3 2892s }; 2892s $VAR1 = { 2892s 'wt_37' => [ 2892s 'wt_37_1', 2892s 'wt_37_2', 2892s 'wt_37_3' 2892s ], 2892s 'wt_GSNO' => [ 2892s 'wt_GSNO_1', 2892s 'wt_GSNO_2', 2892s 'wt_GSNO_3' 2892s ], 2892s 'wt_ph8' => [ 2892s 'wt_ph8_1', 2892s 'wt_ph8_2', 2892s 'wt_ph8_3' 2892s ] 2892s }; 2892s Contrasts to perform are: $VAR1 = [ 2892s [ 2892s 'wt_37', 2892s 'wt_GSNO' 2892s ], 2892s [ 2892s 'wt_37', 2892s 'wt_ph8' 2892s ], 2892s [ 2892s 'wt_GSNO', 2892s 'wt_ph8' 2892s ] 2892s ]; 2892s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.wt_37.vs.wt_GSNO.EdgeR.Rscript 2892s Loading required package: edgeR 2892s Loading required package: limma 2893s Using classic mode. 2895s null device 2895s 1 2895s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.wt_37.vs.wt_ph8.EdgeR.Rscript 2895s Loading required package: edgeR 2895s Loading required package: limma 2896s Using classic mode. 2898s null device 2898s 1 2898s CMD: Rscript Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.wt_GSNO.vs.wt_ph8.EdgeR.Rscript 2898s Loading required package: edgeR 2898s Loading required package: limma 2898s Using classic mode. 2901s null device 2901s 1 2901s cd edgeR_outdir && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl \ 2901s --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt && \ 2901s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt 2901s 2901s 2901s ** Found 2062 features as differentially expressed. 2901s 2901s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR -m diffExpr.P0.001_C2.matrix --log2 --heatmap --min_colSums 0 --min_rowSums 0 --gene_dist euclidean --sample_dist euclidean --sample_cor_matrix --center_rows --save -s ../samples.txt 2901s CMD: Rscript diffExpr.P0.001_C2.matrix.R 2901s Loading required package: BiocGenerics 2901s 2901s Attaching package: ‘BiocGenerics’ 2901s 2901s The following objects are masked from ‘package:stats’: 2901s 2901s IQR, mad, sd, var, xtabs 2901s 2901s The following objects are masked from ‘package:base’: 2901s 2901s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 2901s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 2901s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 2901s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 2901s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 2901s tapply, union, unique, unsplit, which.max, which.min 2901s 2901s Welcome to Bioconductor 2901s 2901s Vignettes contain introductory material; view with 2901s 'browseVignettes()'. To cite Bioconductor, see 2901s 'citation("Biobase")', and for packages 'citation("pkgname")'. 2901s 2902s 2902s Attaching package: ‘fastcluster’ 2902s 2902s The following object is masked from ‘package:stats’: 2902s 2902s hclust 2902s 2902s [1] "Reading matrix file." 2903s for plotting:: min.raw: -0.643115788375154 max.raw: 1 2903s null device 2903s 1 2904s for plotting:: min.raw: -7.50284849776958 max.raw: 7.50284849776958 2904s null device 2904s 1 2906s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_37-UP.subset 2906s sampleA_mean: 5395.606 1816.62 1412.697 637.4673 1681.385 1262.588 20787.35 1013.064 502.9777 665.289 620.238 1371.045 470.179 1407.266 3549.085 1046.9 6030.232 296.1627 982.539 1833.283 4954.434 499.8527 1120.621 2191.464 1037.645 838.8547 581.2863 484.398 522.8673 559.8297 887.2083 1326.5 4776.171 2460.887 335.7477 810.3883 533.844 854.0897 781.6647 198.9307 11423.35 5637.134 333.5833 400.0377 2059.192 562.1487 1319.258 545.5957 480.5827 1066.12 335.4993 409.7437 244.753 1532.142 647.4437 4182.673 134.168 5797.692 1445.705 323.5933 1707.219 4784.861 301.1237 350.1547 15024.4 567.2883 231.4073 1512.754 350.3023 198.8237 298.6353 629 923.62 564.1773 604.7417 363.4713 252.8977 494.789 122.4237 249.8873 114.123 338.9207 508.1423 322.1607 104.2153 150.8137 114.485 148.374 219.039 2602.336 207.4947 180.1727 162.433 2465.916 310.3963 933.0403 1088.069 1272.664 323.2733 762.2617 2891.881 941.4197 425.4187 393.785 241.211 178.6107 388.648 2616.495 872.2057 490.2657 2442.782 203.246 1265.232 772.306 530.7697 4913.275 209.749 89.249 4534.064 335.2157 182.1447 419.6373 876.645 373.2207 335.637 1939.628 1291.39 3468.578 85.82433 456.1583 1326.869 1718.763 2635.243 4713.887 127.1483 731.256 211.844 742.0153 1753.538 583.6803 218.991 579.459 201.4867 122.234 914.4587 1315.006 124.028 744.858 177.4467 2207.998 1229.376 339.0793 693.0703 1640.267 134.0677 599.1197 481.5627 167.1063 579.619 435.0017 719.3537 310.3323 584.709 300.3533 172.982 482.3557 119.932 574.8767 272.6143 122.591 221.959 183.172 99.45067 156.8307 197.342 2446.14 262.1497 340.5557 243.326 323.746 455.3783 161.9753 991.437 71.71033 2002.536 97.82467 154.4447 1214.03 446.9747 303.8613 352.3153 210.486 711.3287 1099.802 912.636 156.591 505.6607 510.4197 1606.153 111.007 407.805 189.715 330.6623 313.843 318.1197 136.2463 354.781 192.5983 1547.728 676.234 432.0453 243.9703 123.246 256.9907 62.65367 356.3497 2688.784 169.0567 112.757 783.8573 387.8127 152.1197 176.9843 196.6567 160.8853 234.695 168.189 62.56033 1125.723 334.935 369.791 690.4453 199.325 146.7767 210.2437 252.697 216.15 328.3217 1815.027 356.783 75.336 563.9263 294.269 60.22767 87.49733 594.819 83.07667 250.2393 617.054 110.791 26.93367 342.712 67.469 109.0817 69.89367 407.6713 83.207 220.177 78.31633 571.859 240.267 207.939 721.5107 239.7997 324.5383 322.742 354.898 421.348 122.177 320.023 160.1673 118.5347 94.07567 97.23167 133.1057 334.361 86.67367 57.64267 86.386 371.817 104.0613 144.7257 76.27033 52.74467 42.552 299.966 135.433 228.911 81.80933 93.672 134.6873 6660.051 115.132 112.5293 1557.898 99.03533 207.397 91.61633 306.508 79.282 110.5993 280.7067 79.07433 307.9013 55.68233 80.98433 363.302 105.6967 78.67633 33.26767 58.232 85.95367 59.60267 76.09067 3561.451 114.563 32.351 94.133 108.859 64.34933 94.69467 155.7297 93.57967 2952.358 172.4453 31.38733 67.206 112.884 64.515 84.25 361.8817 84.972 37.59833 31.766 38.966 84.98533 603.3643 551.5827 526.9727 80.43867 158.1847 87.15633 66.88467 98.302 77.01533 91.79433 73.085 398.1303 422.5397 100.0123 35.384 442.0453 44.71033 204.481 46.65767 41.339 39.99867 47.17133 73.806 74.26433 89.883 62.81 38.21567 31.01767 164.921 280.1693 69.21367 56.34967 703.739 64.40333 21.82767 69.72667 1172.149 30.17067 405.356 37.93767 112.7063 47.40267 51.06833 84.101 144.1087 340.941 38.01367 67.623 279.711 58.726 103.086 176.214 34.95267 306.441 32 32.60533 197.0237 20.93567 44.67767 40.988 246.2103 36.76933 31.13533 52.91967 53.25667 39.204 56.22233 74.20533 71.85 32.07433 15.402 9.429667 49.19267 38.41333 69.92267 37.304 5495.505 30.96067 66.12467 78.667 43.95233 38.414 131.435 47.775 95.708 40.022 16.46033 23.42167 171.2653 69.90667 85.27667 56.78633 84.52867 54.81767 65.34533 50.27133 51.916 27.49133 163.5027 52.662 28.112 115.2073 24.04867 168.4167 31.93633 33.50367 89.08767 52.49167 71.55767 8.473333 29.75167 34.237 35.23567 14.64167 38.44933 10.73367 42.42 16.59667 36.44033 23.565 158.4163 15.47467 41.489 20.16567 209.263 88.74833 23.62733 56.72833 26.74467 43.001 40.90567 24.90267 40.95667 16.558 19.56433 66.32833 14.972 14.82667 23.34767 22.18367 23.36033 16.066 16.92233 36.86033 20.61433 27.81033 68.59733 27.801 31.332 10.08733 18.50767 35.217 46.006 22.395 23.232 32.359 59.42267 23.66867 33.16667 23.236 36.55567 9.629333 59.42133 21.92233 12.32167 49.753 21.21933 67.70667 176.112 16.79467 28.812 18.73767 39.53833 28.092 45.49933 21.19933 15.77833 17.69467 25.49633 29.40667 19.11367 15.04667 9.539333 13.554 22.47933 73.985 13.172 26.41767 23.48733 30.22433 11.36333 13.02633 23.85333 21.16733 17.51267 24.04533 28.304 5.914333 21.95267 18.054 19.42533 2906s sampleB_mean: 4.127667 3.202333 4.412333 2.778333 10.849 9.133333 336.3973 18.23967 9.088 12.67333 12.49967 28.87167 10.76867 33.63533 84.42267 27.41467 173.6673 8.580333 33.35533 63.97333 175.7007 18.18567 43.62667 98.61433 47.461 39.777 27.60133 24.33867 28.62567 32.483 55.41567 98.97567 543.417 73.97767 21.376 63.963 47.52733 11.05733 4.512667 5.223667 534.2237 68.49367 36.39433 24.273 313.6673 52.09567 117.2063 72.053 39.797 183.983 2.287 42.68733 5.388667 225.2773 49.48767 658.8357 13.52433 900.1817 139.4193 38.47567 218.998 299.0663 55.75367 36.41067 661.7387 23.51433 7.825667 281.149 19.23033 22.41533 26.58267 94.08633 79.21633 68.27467 95.47967 12.30667 15.51133 58.90833 3.616 36.231 2.461333 50.10333 79.409 6.660667 14.398 10.44 2.967333 9.605 9.034667 514.415 28.87667 27.94467 11.277 7.979667 29.69867 143.4493 145.798 217.05 25.39133 43.57767 125.8543 232.083 72.874 68.88567 22.455 32.70533 85.85133 629.0693 116.6427 44.471 563.4113 32.93 250.9827 68.979 110.7323 1003.238 15.964 1.321667 3.101333 43.422 18.134 50.429 94.216 53.687 74.29867 297.3653 194.2893 457.8803 10.49667 80.21667 191.8153 296.743 623.5437 338.805 14.087 170.8453 29.54433 62.58133 375.202 85.73633 48.99067 102.7107 23.402 10.49233 213.755 131.764 15.837 132.8633 21.00533 412.998 124.0153 70.59233 150.937 280.8763 23.18133 130.483 105.7627 33.283 113.0753 66.97833 119.1803 21.807 122.476 29.063 6.052333 70.27367 22.87333 56.695 38.81867 8.546333 45.02367 26.18 10.675 2.732333 29.96067 582.8023 40.96933 72.46567 43.417 38.353 92.838 35.82667 223.4383 10.603 429.5973 10.31967 37.50533 230.2087 88.46167 49.50333 56.458 32.109 118.5947 170.561 115.6623 30.82233 118.5987 126.7297 6.318 11.71333 58.22233 31.15267 43.27 74.91 73.76233 14.554 80.928 26.01033 377.1183 116.0857 70.388 60.89033 29.317 62.40367 4.263 58.833 462.724 14.82467 12.85033 170.3357 89.28567 26.68733 39.035 42.91667 14.26033 45.62033 28.625 11.399 261.706 64.78933 70.13033 154.972 20.14333 32.132 28.455 52.69567 45.433 43.231 402.3693 68.36967 6.437333 120.0037 55.04367 12.03667 6.740333 131.159 18.13133 48.89067 115.9157 26.685 0 71.40267 8.652333 19.12733 8.867667 96.276 20.623 16.50567 14.54933 87.39733 44.52567 51.52233 80.658 41.856 55.915 73.756 7.045667 75.955 19.68333 71.137 36.07133 28.90033 12.35967 22.98467 24.22767 72.094 17.759 13.374 15.947 78.80367 16.69133 29.59733 15.62833 4.583667 10.51167 72.38467 15.437 40.359 10.94967 16.16267 31.58467 938.454 26.14833 15.32067 260.6453 19.23 47.833 15.559 71.361 17.413 16.40267 65.26833 12.544 65.235 7.72 15.42567 64.46467 15.246 7.913667 6.353667 8.792667 20.73367 14.42733 14.33167 499.6263 26.33733 7.566333 19.81633 21.776 15.44967 18.174 27.02667 18.108 424.5863 32.75133 6.926 12.19033 14.411 0.6243333 14.04867 69.556 14.10833 3.122 5.709667 9.231 18.931 118.617 19.63133 73.07533 19.83467 28.212 14.08133 7.66 12.226 14.676 19.28233 12.023 84.71567 1.723667 16.38067 2.032 40.53433 7.395 40.363 10.23033 9.647 6.174667 10.679 11.486 17.83733 21.74733 12.327 6.723333 2.410333 28.223 20.15033 10.57833 6.977333 138.602 9.925 0.8883333 13.91533 228.7547 7.087667 22.77967 2.177 22.84267 8.274 7.516667 5.474333 21.41267 67.14133 9.294667 15.98533 58.535 2.115333 23.04733 17.25667 5.981333 72.50367 7.807333 5.685 37.02633 2.503 9.524 4.98 14.50533 3.465 5.992 9.865667 8.352 8.836 9.195667 13.76033 15.521 4.789 0.4626667 0 8.369 2.327667 8.412333 4.895 10.288 5.838 15.28167 17.55633 10.124 8.525667 21.67067 11.013 23.05433 4.636667 3.596 5.664333 21.40333 11.173 15.31167 5.468 4.385333 13.31333 13.338 10.828 10.462 6.127333 23.191 8.300333 1.195 9.423667 1.734333 29.664 5.784 7.374 9.302667 9.638667 13.186 0.093 5.607667 8.232 5.763333 3.51 9.153 0 6.257667 0.668 1.998667 1.755667 23.73867 3.68 5.190667 3.966667 18.65833 10.806 2.341667 6.641667 1.905667 10.293 5.354333 5.709333 4.074333 3.201 2.98 5.685333 2.939 3.158 0 3.513333 1.651333 1.586 1.497 4.132667 4.44 3.141333 5.035 0 0 0.5686667 2.188333 4.641667 3.210667 3.095667 0.1823333 7.557333 10.216 5.790333 7.033 3.540333 6.03 2.409667 13.56433 2.302 2.956333 7.787667 1.153 13.44 8.689333 0 3.694 0.983 6.688 5.750667 10.00833 4.922 0 2.606 2.441 5.14 0 1.536333 0 2.830667 4.562 15.67833 0.6903333 4.982333 3.702333 0 1.582333 1.234 3.677333 2.279 1.876667 0 6.093667 1.506333 3.117 0 1.735 2906s num discordant: 0 2906s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset 2906s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_37-UP.subset) passes test. 2906s sampleA_mean: 0.838 2.696667 3.078667 2.398333 20.01233 2.713333 16.51667 4.654333 7.951667 15.838 279.6767 5.762333 98.85333 13.98533 68.104 691.0767 20.97667 72.55133 103.6867 96.61333 558.1363 526.2243 17.37067 539.652 81.319 641.1777 96.77733 251.019 300.087 620.406 478.7223 1406.461 226.9223 536.193 38.978 35.44767 45.76333 4.080333 11.583 9.434667 5.017333 21.39933 7.282667 93.42833 213.4847 33.62067 113.178 15.04567 850.6397 57.26933 7.212667 1005.984 1005.984 876.482 37.25567 40.61467 114.5207 98.448 733.6827 37.255 3.139 57.579 655.8127 967.4877 915.841 903.1557 18.754 4.244 39.57833 128.1763 7.601333 2.177333 866.6187 10.53633 954.153 31.501 62.50533 509.7623 103.9153 70.24967 37.21967 409.1913 27.52967 18.30633 224.904 555.952 27.29 1117.319 29.18933 2.280333 861.8193 33.57133 884.0843 1220.149 28.45833 76.41333 551.9577 260.666 2.592667 16.528 3.516 5.682 20.36667 18.88733 7.412333 1784.069 950.0057 121.0697 360.2233 10.30533 18.96267 4.745 94.089 25.55733 14.91467 56.797 2042.114 642.0663 15.73033 504.111 22.627 27.48633 39.67767 1690.757 443.633 17.221 86.883 6.546 6.496333 44.93767 29.55 35.29633 4.361 1385.135 6.167 3.586667 5.016 866.9083 67.08167 75.48133 1545.514 1.292667 7.963667 17.48067 1.460333 6.515667 1.919333 5.627 3.595333 35.529 223.9227 237.8803 65.027 77.21567 1681.069 425.357 141.697 22.92133 71.78533 20.37167 94.847 9.896333 6.455667 43.09833 617.7277 697.2287 100.1173 3.451 393.3037 23.04333 27.23133 16.54033 27.59267 1094.775 188.4693 5.802333 11.52 560.8327 6.300667 50.14667 64.19 129.326 2466.545 16.27833 47.34533 5.474667 31.92667 22.74167 660.21 1313.1 1593.583 66.65833 63.58333 503.5693 43.50567 15.54567 15.08833 37.942 15.92433 42.57533 1584.902 23.33733 7.685 9.969333 14.33333 1834.914 898.047 51.407 2590.581 9.613667 40.12067 0.8066667 30.828 603.456 337.399 42.16667 6.745333 118.9327 18.233 12.30833 670.486 3.979 20.135 18.592 7.059 2.433333 134.6073 5.557333 7.980667 1.574667 443.3597 91.49933 7.909333 40.25467 74.00233 23.09367 28.839 34.16433 46.75733 40.23433 2.900667 17.96533 4.531333 4.281667 123.0927 110.725 759.571 6.527333 48.27367 302.136 14.71933 9.824333 8.791 1.991 824.9103 6.812333 73.27533 225.547 50.11167 73.59667 2.154 47.651 6.250667 61.43567 11.312 1666.136 22.68433 27.61367 9.274 15.46533 15.18033 13.78833 1796.241 7.252667 25.71133 0.1093333 354.6413 18.317 4.766333 12.40267 46.23067 6.929 1846.256 18.67133 49.835 474.4033 44.97967 25.208 22.375 93.21667 33.815 46.17067 7.083333 759.148 43.83633 2166.993 5.733 10.12033 36.11867 19.73 8.807333 28.26467 497.7577 27.77367 251.833 0.713 29.26167 109.3627 23.127 2.068 24.63167 48.562 17.59867 34.33067 1.851 66.73133 25.73033 3.200667 325.5413 11.93267 15.25233 8.292 6.248333 35.802 2.811 30.97967 9.767333 20.71867 13.58 7.869333 59.43533 11.286 21.67167 7.107 17.53667 7.48 3.762 8.395 43.001 112.283 8.866333 13.64567 33.21467 25.40433 2.682667 18.33267 483.664 8.631333 5775.202 8.002 87.024 49.788 46.73367 14.93733 25.089 321.257 22.31833 6.686 275.3867 11.98267 5.931333 5.558333 20.81133 9.773333 4.59 5.895 756.3963 3.293333 12.79833 37.152 6.863 5.603 16.116 15.94867 25.32233 16.64833 17.85933 31.12967 16.899 2.163667 48.976 21.32033 30.75333 1001.993 15.01 26.40167 7.782667 9.616 7.700667 27.14367 7.766333 5.615667 16.66533 4.341667 27.53867 15.57933 6.204 2.723 21.74467 5.364667 2.800667 7.226333 4.926 12.36433 21.06767 27.83967 0.9146667 8.077 8.316667 16.73 2.534667 16.303 11.22367 20.261 12.753 25.646 266.444 11.40267 12.443 10.471 18.23433 1.695333 275.0887 22.93933 7.884667 1.688667 5.415 4064.721 74.79833 14.18933 13.22967 14.558 14.83533 1.160333 12.76533 2.243333 5.740333 1.288 12.44167 6.091333 7.310333 10.85033 1956.885 9.105333 16.40367 24.758 95.166 11.22367 8.028 13.71433 7.039 2.194 1.577 3.424 9.510333 20.74967 11.59067 11.227 12.90733 22.17067 5.421333 0 6.524 7.844 13.917 2.818 8.791667 12.394 3.109667 13.106 5.630333 20.36133 2.411 6.559667 0.248 6.380333 7.672667 1.302333 7.621667 9.378667 9.436667 8.497 26.291 1.363333 12.388 63.63933 7.711667 11.91033 4.676 34.157 3.857 9.471667 8.578333 17.75767 6.778333 3.294667 13.65367 13.50467 12.14267 6.625333 6.567 10.72933 6.067667 16.556 3.09 8.293333 5.416333 6.861667 5.332667 7.431333 6.829333 0.409 6.066 0.01 6.512667 0 7.585333 9.694667 10.12333 17.19233 2.758667 11.94067 11.36067 11.758 7.325667 4.963667 23.38367 3.468 11.994 9.299667 0 5.177333 3.165 9.557333 12.01933 3.493 2.976667 3.268333 1.407667 6.521 4.482333 3.736333 1.911333 19.73733 0 4.695333 3.301333 7.337333 39.729 3.822 3.489667 11.46067 10.216 0 5.422333 26.67367 5.633333 8.411333 4.053 2.467333 1.547 8.805333 0.4346667 11.24533 15.47733 1.897333 10.201 4.765 3.680333 0.7683333 15.75333 8.445667 1.384 4.638 9.507333 3.27 2.745 17.23067 6.326 1.184333 5.581333 6.395 4.293333 0.6643333 1.870667 2.14 3.051 2.550333 2.219333 6.813333 4.127333 1.252 2.517333 0.3906667 6.606667 4.484 2.605 2.330333 4.196667 8.839 1.153667 3.021333 1.56 5.001333 2.578333 1.169 2.448333 9.374333 7.634333 2.692333 4.009 5.019333 12.573 4.196 0.9123333 4.223333 2.011 3.043 8.218333 0.724 3.090333 3.162667 35.57467 1.351667 4.126 1.122 9.984333 1.344 2.242667 21.42967 1.469333 2.678 3.484667 8.963667 3.986667 4.744333 7.756333 8.504333 1.637333 0 4.41 2.573667 1.836 3.393667 8.025 4.724667 11.52467 5.509667 1.089 3.328 2.804667 1.696667 1.980333 35.02267 3.398 10.61867 2.523667 2.844 0 3.077333 2.577667 0 3.570667 3.682667 2.056667 0 8.773 1.863 8.003 19.30967 2.877333 1.994667 0 1.978 3.945667 1.784333 0 1.102667 4.313333 3.675333 0 3.851333 4.52 1.800333 2.192 2.335333 4.102333 3.773 4.021333 0 0 0.989 4.572333 10.20033 5.391333 12.372 1.697667 2.944667 0.768 1.092333 9.440333 0 1.981333 0.3666667 0.5473333 2.347333 4.55 9.496333 1.414333 4.251333 0.8833333 0.7693333 3.630667 4.372 2.943333 2.396667 0 6.084 2.881333 2.291 14.29267 2.337333 0 1.477667 0 2.404667 3.280333 0 2.190333 0 3.352 1.992 3.248333 0.9593333 0.4253333 7.155333 3.064667 1.162333 2906s sampleB_mean: 381.073 324.8553 363.4697 136.0917 1076.978 135.6287 721.2523 193.995 322.6313 501.0717 7779.492 155.6753 2550.414 340.8923 1492.051 9939.373 303.273 1007.03 1438.471 1331.648 7520.41 6944.853 217.5877 6464.644 973.0083 7181.47 971.4367 2449.757 2827.345 11165.49 5346.478 10849.9 2510.784 3982.392 347.4017 722.7793 440.9727 204.688 188.059 227.1767 183.432 341.9023 304.1167 1192.947 1506.715 318.3057 1781.496 147.2877 6705.697 644.756 98.27667 8614.152 8614.152 6887.084 636.1717 510.9113 876.8277 819.1427 5036.385 568.9407 293.4293 512.042 4540.328 5874.642 6156.043 5974.238 176.1237 88.77667 381.4813 850.5097 204.598 132.997 5515.698 224.959 7405.14 297.5633 820.1 3398.294 803.7297 493.2167 337.5617 2649.173 374.99 728.6047 1237.565 3104.744 347.1993 7596.105 568.3683 91.93733 4809.412 286.7303 5589.41 8313.711 464.25 395.6523 3325.992 4978.607 199.5333 210.5073 615.4837 190.3363 237.9167 234.8707 327.728 8625.824 8726.054 1183.775 4624.974 254.0923 165.5147 177.6103 592.331 229.8227 307.597 498.566 12136.75 4181.758 126.265 3101.543 257.8713 318.668 437.8937 11956.17 2806.072 209.5997 880.4753 124.821 96.888 330.2803 178.331 265.4807 565.0517 10695.83 59.968 107.6607 133.1137 5311.835 497.3057 369.4417 9160.812 65.022 189.81 361.7567 66.28233 240.9067 79.23 148.3807 92.04867 277.6277 1388.008 1147.187 744.834 617.5097 10005.84 3135.76 624.4283 177.0987 437.7077 169.5693 501.203 130.7987 163.2497 365.9053 3477.406 5150.462 464.656 85.369 2813.865 227.959 396.4167 159.9217 248.7967 7921.826 1232.959 87.30767 139.8577 4052.112 58.786 223.6213 303.588 784.5 12803.12 201.1477 309.0137 129.359 205.964 151.089 3606.195 8077.68 7646.521 365.304 366.6233 2069.238 242.2357 196.2657 102.4913 198.0453 171.415 221.5063 9231.562 146.225 53.11833 76.629 198.031 11807.78 7137.863 346.0203 14596.83 141.1233 244.213 94.084 221.3943 3043.903 1727.754 228.616 115.6383 954.507 134.7863 186.3673 3497.592 343.3797 171.2443 160.6447 118.4783 176.1103 794.7277 41.92667 79.78767 374.3023 2899.79 383.3883 132.86 243.0527 434.0653 332.1927 204.0893 383.105 306.1523 259.974 56.084 153.6373 102.4957 160.461 566.3103 473.468 5955.872 138.7943 297.5293 1314.765 93.961 165.6487 92.801 88.20067 5402.498 175.727 376.801 1374.415 208.997 324.095 38.50333 219.043 578.1793 261.1813 166.719 7998.991 145.871 146.7367 109.0163 88.84733 106.9733 112.8707 7391.381 55.56067 217.828 58.52433 2636.168 92.66933 82.77467 110.12 199.25 65.82467 10466.26 84.19433 317.4007 1924.887 506.512 434.5497 162.353 434.0367 264.5573 241.8647 51.48067 4659.391 279.8187 12057.81 79.15267 104.7473 210.276 108.0163 44.52667 130.4647 2478.864 219.1713 1538.062 60.909 120.016 502.0593 125.9207 54.28 102.9103 404.8233 102.8277 189.876 59.07767 288.2643 109.1297 67.97633 1485.8 92.14267 138.9953 71.07333 65.14433 221.9553 42.94067 155.6507 63.51467 94.855 205.7273 49.84633 451.6893 139.4217 91.36867 72.27033 88.724 53.67933 136.3853 91.96267 251.6407 446.5917 101.2043 142.4997 147.5143 150.83 64.48933 125.6427 2983.166 98.42267 31019.62 72.04033 391.7213 217.945 244.312 114.7247 313.5353 1573.052 188.654 92.354 1190.783 54.17467 98.59367 78.15767 138.8203 94.036 57.92467 72.229 3680.324 57.289 71.95633 329.0943 48.662 284.8557 359.4497 117.3687 147.9097 112.4907 89.19033 160.033 80.658 323.135 272.869 177.7223 205.2823 6554.638 75.13167 143.6177 67.32633 92.10033 55.31033 111.3283 92.91767 71.83833 92.673 58.84033 123.7103 83.32767 68.93667 64.96333 97.74133 33.64933 66.58633 63.519 86.666 61.75633 114.413 126.6667 61.049 52.40167 62.202 70.82967 31.92033 558.288 54.697 97.67333 98.25867 189.338 1437.071 86.82867 55.42833 51.40267 185.3687 26.105 1768.526 143.2053 69.31567 27.42533 36.84367 23095.85 654.0063 106.367 92.58367 84.09433 63.39167 29.412 65.265 25.16133 49.55567 23.09333 59.70833 30.305 61.927 60.39433 12433.72 44.59133 91.34767 108.9977 629.935 47.69867 37.13833 80.30267 59.309 38.35733 21.31667 36.129 40.01867 97.91867 56.87433 100.9357 74.47967 101.2333 40.88467 41.25767 29.19933 44.65167 75.314 81.03933 67.40867 63.275 52.62167 70.48667 28.11233 89.473 20.836 65.641 18.746 57.89033 36.83567 63.43233 39.14833 51.208 50.94033 37.861 105.9517 33.71767 82.208 269.8203 37.373 59.017 45.43467 180.145 46.01667 53.35367 51.20733 72.092 38.239 17.67167 58.72433 70.23367 118.5717 36.76167 40.58467 43.553 48.09067 104.9537 32.39167 95.03067 31.81733 74.76 24.105 42.02167 63.80367 40.14133 44.57067 16.39933 134.3513 17.20333 57.38933 44.80233 52.59533 71.77333 37.18267 49.809 60.34067 83.02567 49.184 24.998 275.1827 22.795 77.42067 39.439 9.080667 42.55233 16.98933 43.199 58.53467 22.759 23.031 134.6853 17.978 31.64467 50.66867 50.351 19.87967 89.41967 8.385 130.2143 28.618 80.83067 170.7703 19.01033 79.93733 147.841 49.53233 101.7453 28.99667 170.258 79.05433 56.735 24.42933 82.00433 27.15533 40.58733 9.165333 59.187 64.17467 17.666 45.68133 46.573 28.08767 12.81233 63.14133 72.57967 45.292 39.557 38.56967 21.26833 25.20967 69.73067 25.818 47.25833 31.359 35.30367 21.37133 12.13567 125.1613 33.96833 19.069 17.60767 16.69733 34.963 31.40267 16.692 26.59233 17.79667 33.96667 38.06967 16.98933 16.53733 18.67167 43.21967 58.21167 51.753 22.82667 38.21633 28.28967 55.27767 37.33167 50.767 62.14133 21.58933 21.925 42.533 122.654 37.97 17.76433 52.68633 70.339 15.914 69.305 23.8 13.31667 13.12667 200.7123 8.173667 18.98967 10.06533 48.78233 10.878 19.56367 133.2117 11.03933 23.558 37.25433 63.401 49.67067 23.01233 37.89133 37.642 14.71567 116.5107 49.08533 22.41933 26.17633 23.021 43.66433 24.04433 76.51933 24.348 8.213333 20.035 27.69933 34.59267 12.07167 139.358 14.291 45.16833 23.64233 13.166 29.38867 30.44067 20.69233 11.09467 15.776 22.33433 11.24133 44.84 51.325 45.16467 34.98133 92.552 12.62967 11.69767 12.82333 35.719 26.364 14.12933 23.75833 27.504 23.05967 57.80667 35.64 26.279 29.65133 17.39633 14.443 18.31433 23.06333 18.868 23.808 7.635333 5.506667 22.85333 21.97667 64.09967 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test. 2906s 29.06367 63.05533 9.625667 16.55933 17.268 15.14 48.198 33.81667 14.02 2.727 14.585 9.959 31.779 43.573 17.85033 27.65767 11.04933 10.03867 28.30367 28.58167 17.96567 16.253 1.073 27.41967 14.46867 9.625667 59.659 14.20067 8.730667 27.819 10.958 11.44933 13.08833 18.55767 21.40767 11.718 35.49 29.841 14.722 16.94833 7.215 40.67867 28.26067 6.225667 2906s num discordant: 0 2906s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_37-UP.subset 2906s sampleA_mean: 5395.606 781.6647 1816.62 5495.505 734.0483 1412.697 1120.621 502.9777 1262.588 310.3963 1751.765 15024.4 620.238 665.289 1833.283 2602.336 6030.232 1291.39 887.2083 3549.085 494.789 637.4673 1371.045 1013.064 499.8527 1681.385 1046.9 1445.705 647.4437 521.84 470.179 2191.464 5797.692 371.296 4954.434 1326.5 4191.816 982.539 944.0123 1407.266 4913.275 12222.46 335.7477 2635.243 559.8297 20787.35 1512.754 2002.536 1265.232 1593.001 854.0897 567.2883 1272.664 154.4447 4784.861 198.9307 116.9527 3468.578 326.0873 36600.33 244.753 258.5643 1348.496 234.695 999.5363 335.4993 562.1487 335.2157 564.1773 933.0403 1939.628 296.1627 178.6107 1233.492 810.3883 4713.887 405.9907 194.6923 335.637 1532.142 1933.215 388.648 581.2863 1088.069 594.819 1718.763 405.4877 393.785 1656.826 104.2153 1707.219 1091.041 5645.434 435.0017 521.2813 499.693 209.749 300.2583 1031.742 387.8127 252.8977 1037.645 3088.486 298.6353 363.4713 923.62 2446.14 210.2437 272.6143 1640.267 590.469 425.4187 176.112 925.3123 4534.064 2891.881 1179.723 533.844 114.123 150.8137 2237.79 344.3147 103.573 146.7767 772.306 122.4237 460.3903 876.645 322.1607 1753.538 531.0443 337.406 233.2683 762.2617 825.5967 122.591 244.4597 581.914 159.0503 337.767 617.5563 133.8673 2017.126 168.438 838.8547 872.2057 1707.261 122.177 1434.927 604.7417 1547.728 610.589 5637.134 89.249 100.0037 568.889 664.8137 356.3497 114.485 508.1423 482.3557 1030.087 480.5827 156.8307 3561.451 1756.628 378.0157 1198.79 109.0817 147.324 199.325 563.9263 89.41233 99.45067 310.3323 432.0453 156.591 349.218 97.82467 219.039 323.746 85.82433 210.486 182.1447 164.5937 350.3023 120.7347 201.4867 176.9843 128.0267 241.211 207.397 94.07567 407.6713 368.628 1125.723 991.437 189.715 719.3537 437.1223 770.6237 125.2723 71.71033 240.267 389.129 164.083 1315.006 324.5383 116.1613 198.061 62.56033 603.3643 328.3217 81.80933 207.939 721.5107 132.971 177.4467 183.172 63.90033 78.31633 316.5037 78.67633 160.8853 52.74467 26.93367 105.1747 127.1483 104.0613 60.22767 2465.916 354.7773 407.805 300.3533 206.046 519.577 161.1783 169.0567 1229.376 294.269 66.11467 91.99833 84.98533 212.7377 94.133 172.982 168.189 250.2393 98.94267 291.7607 124.4867 1099.802 132.1053 129.574 471.4763 562.891 115.35 421.348 59.607 236.6537 280.7067 1557.898 1606.153 181.09 173.3993 93.672 354.898 278.785 87.49733 154.7137 60.025 76.27033 55.68233 98.85333 363.302 93.57967 136.4807 86.272 62.65367 90.65667 40.38733 171.9977 105.6967 80.98433 2036.308 73.156 304.6523 1505.046 305.3177 51.06833 280.1693 204.4367 38.966 113.344 971.5327 214.102 46.29267 425.4893 53.23867 87.15633 95.84833 77.01533 44.27933 54.279 66.88467 66.544 135.433 62.81 56.42633 64.515 407.7717 35.384 97.46133 38.21567 471.7457 6075.931 751.6327 47.17133 74.26433 233.2737 69.30367 32.07433 194.3693 144.1087 630.4887 86.26767 47.40267 16.066 171.2653 93.98167 33.614 56.34967 69.90667 26.77667 27.49133 38.41333 158.4977 44.67767 40.022 101.362 50.39 71.55767 187.0867 58.726 115.2073 51.916 31.01767 32.60533 71.85 84.101 37.746 40.76933 114.1953 30.31033 37.93767 35.92467 141.5087 56.78633 50.27133 131.435 42.52667 82.45067 47.12267 42.259 49.19267 51.68567 56.986 58.77867 34.524 422.5397 496.4993 41.489 7.951667 38.467 51.49667 209.263 163.5027 70.90433 33.66067 45.27567 27.86967 42.42 34.55067 52.054 26.74467 51.36633 56.72833 32.359 48.80533 10.913 142.1963 36.76933 19.379 32.87767 43.001 19.36133 42.69267 269.428 52.49167 45.48233 66.32833 69.761 20.61433 59.42267 26.72567 24.04867 45.49933 28.092 84.52867 73.985 59.42133 40.90567 31.80833 36.44033 27.07933 20.94233 86.196 132.0313 38.71367 23.675 28.112 36.69767 27.81033 13.58767 20.89067 13.46233 27.92067 14.06933 27.10933 23.51567 31.895 32.296 43.59833 23.62733 19.87867 22.01133 23.94367 30.83533 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_37-UP.subset) passes test. 2906s 27.801 36.86033 24.69267 45.54267 27.52167 9.022333 16.59667 20.281 68.59733 191.9503 26.41767 14.442 22.18367 27.188 11.48267 26.73867 29.40667 20.15333 25.49633 23.232 13.54667 23.66867 22.07333 20.21567 18.73767 20.84167 44.083 37.072 13.02633 26.52667 40.67567 18.52533 13.554 14.434 41.65 20.87967 8.334333 18.24067 12.43333 15.60267 28.812 16.92233 30.77433 15.976 35.217 8.423667 35.653 15.92 17.69467 67.70667 17.132 28.27267 25.093 22.21567 19.03867 25.03867 46.006 38.67233 25.646 27.70233 20.36367 66.471 30.20433 24.57 15.579 21.81067 12.36533 26.937 24.97367 19.224 10.894 12.97133 51.373 20.40767 56.10667 11.617 18.127 15.803 26.99167 20.359 36.983 13.338 23.34767 9.058333 20.34733 23.038 2906s sampleB_mean: 4.892333 0.8923333 3.02 10.731 1.413333 4.947333 4.916 2.201 5.897667 1.439333 11.541 126.2827 5.31 5.982333 18.24467 28.83167 71.58533 15.897 11.73133 54.76233 7.353333 9.523667 20.785 20.73967 10.32667 34.85667 21.734 39.02467 18.007 15.272 14.071 67.15133 190.2367 11.974 175.0553 46.38933 162.736 38.35033 40.62 61.93367 231.01 644.6073 17.87533 149.0183 38.834 1576.856 120.2997 60.698 70.315 84.69133 10.01733 5.055333 122.321 6.593 176.7203 5.075 6.833333 143.0547 34.29367 312.258 4.303333 20.43633 62.01667 6.119333 52.632 2.999 41.809 18.10167 44.774 82.944 191.4833 21.86767 17.35367 131.954 97.40133 184.242 33.76633 11.08667 31.756 216.263 91.85267 51.789 69.84367 85.388 21.75133 167.6013 68.43533 46.20633 70.838 10.803 199.414 78.63867 1058.536 18.98533 34.63 5.957333 6.52 8.328333 146.7283 32.09667 13.45833 154.1127 8.807333 29.81633 18.10667 94.25133 327.4777 3.039667 14.93967 172.0003 19.323 62.69867 10.14033 167.5307 1.982 107.587 120.642 99.03833 5.291 13.40767 176.0093 48.44967 1.620333 9.162667 52.029 7.044667 86.94433 96.643 17.25433 290.869 59.39767 44.574 22.66633 60.149 138.9923 5.435 33.99767 81.38067 29.81667 57.83967 35.93933 18.47767 263.582 24.10267 157.5777 151.9077 274.274 3.384 147.5103 135.326 296.326 119.8197 585.796 5.086333 7.705667 98.93967 138.5447 45.153 12.202 111.2203 78.18267 236.2837 81.65333 3.080667 52.72333 288.293 60.40333 112.516 9.454333 29.03533 11.36967 71.425 11.83333 11.37767 36.04767 62.152 25.95767 81.69867 10.11133 31.115 40.80033 16.697 33.16933 31.26267 15.18533 68.39567 4.436 37.04267 33.04933 15.958 52.859 22.379 4.922 77.499 77.462 239.1367 228.12 31.045 131.7207 64.78833 76.85 22.86333 14.63133 46.24133 52.96867 29.20433 252.1407 44.73367 26.55867 43.10367 9.876 32.20767 46.83533 6.152333 42.20867 64.61967 21.17867 41.19767 41.53733 12.78767 11.56533 66.14267 2.519 19.13967 3.457 0.388 20.32033 28.43733 14.93967 12.457 192.615 81.672 80.735 55.72533 27.23467 68.06833 33.53433 24.19267 252.5313 60.023 3.929667 21.33367 11.13 22.53 13.001 27.607 37.84833 50.52767 15.63733 49.06433 21.97267 262.4237 28.67333 25.094 103.8797 92.249 24.55133 77.08667 9.053333 53.45667 57.499 221.51 129.8027 29.328 41.26233 16.52467 10.47367 38.40433 16.72967 36.59667 12.56167 17.05033 8.892333 16.70467 72.445 15.72 23.92933 4.478333 14.59467 15.84233 7.813 26.382 19.338 16.686 456.8783 3.546 72.39567 300.8857 58.95767 3.424 10.048 41.21667 6.782 26.43 161.046 49.04333 6.808667 38.81867 9.581333 10.136 20.181 15.967 2.343667 9.956333 10.61567 15.178 30.64367 11.71167 6.818 3.776 79.67267 2.932 19.69133 7.134 63.54133 603.3247 131.0337 10.08733 14.317 47.94933 12.49533 2.596 41.753 22.72933 144.8737 13.70767 9.795333 0 6.163 11.88467 5.698 9.696333 4.551667 6.056667 3.111 0.77 24.952 9.568 2.558333 8.861667 8.024 6.153 44.787 3.721 0.8253333 9.442 6.028 6.225333 15.87967 9.684333 7.286 5.855333 25.736 5.053 5.482333 5.451 5.704667 5.819667 9.387667 23.79767 8.245667 12.136 10.034 6.709 9.898 11.101 3.947333 13.348 6.474667 25.345 96.05 1.601 0 2.289 3.487 9.86 30.05333 15.06367 1.628667 10.75867 5.932 5.672667 4.229333 9.460667 0 10.76167 2.356667 1.994333 4.762667 0 34.28533 2.515333 2.445 6.930333 6.886 2.312667 6.758333 60.65633 12.28333 4.818333 2.695333 16.034 2.932333 3.923 4.023 4.175333 3.518 1.379333 18.601 3.183333 8.966667 4.880333 5.966667 5.916667 0 0.597 1.362 26.49267 8.657333 0 5.907333 2.795333 2.091333 0.3683333 3.392 2.201333 2.298667 1.082 0 1.805 5.972667 6.506333 10.182 3.766667 3.583333 4.613333 4.885 7.344667 0 4.728667 0.911 4.943333 2.479333 0 2.582 1.481667 7.661333 47.94667 2.759333 0 5.132 3.599 1.101667 2.819 3.284667 4.356 0.774 0.3263333 0 4.525 3.673667 1.016667 0.7583333 2.833333 8.528 7.471 0 1.173667 5.924 1.954333 2.414 2.116667 2.037 0 0 3.214 2.062 2.585333 2.919667 3.048 7.372333 3.673333 7.599 0.05333333 7.766333 3.431333 2.400667 16.083 3.17 0 4.567333 3.38 2.839333 4.954667 9.191667 3.975 5.980333 4.509333 3.139667 16.31167 1.766333 2.267 2.893333 4.752333 0 6.575 1.525 0 0.969 3.08 8.722 2.136333 7.809 1.796333 0 3.779333 1.799 2.693333 2.451 0.7883333 4.770333 1.826 4.1 0.831 2906s num discordant: 0 2906s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset 2906s sampleA_mean: 15.838 2.068 4.080333 21.39933 36.11867 7.282667 7.963667 2.713333 7.685 16.51667 6.167 5.415 40.988 88.57 10.53633 102.2703 31.261 15.04567 28.64033 72.55133 96.61333 103.6867 30.97967 20.01233 224.904 68.104 141.0787 509.7623 2.398333 5.762333 4.654333 46.17067 76.15267 0.1093333 16.54033 121.0697 37.21967 2.433333 4.281667 18.96267 55.26267 7.252667 98.448 40.83233 803.1917 503.5693 25.78433 57.26933 9.434667 539.652 26.51267 4.244 0.4346667 526.2243 11.583 279.6767 1.292667 3.451 7.212667 655.8127 291.1757 478.7223 0.713 2.550333 11.22367 504.111 31.92667 88.20633 558.1363 15.54567 14.71933 35.44767 337.399 5.017333 81.319 31.501 11.52 409.1913 3.200667 96.77733 5.627 26.208 125.9483 2.219333 40.27 24.615 20.97667 733.6827 13.98533 45.412 354.6413 9.896333 25.605 3.586667 578.8703 5.474667 78.96333 22.74167 31.97667 1.577 2.280333 47.34533 5.682 1.460333 300.087 3.078667 43.50567 915.841 115.4593 3.420333 23.127 33.57133 48.562 23.33733 903.1557 20.36667 25.208 50.11167 0.838 43.09833 40.25467 188.4693 1275.026 697.2287 37.152 443.633 641.1777 2.243333 7.980667 6.745333 3.595333 16.528 113.9973 12.94133 6.515667 23.04333 34.135 33.62067 17.48067 763.5533 28.26467 12.993 7.059 620.406 0.8066667 106.1753 5.016 6.546 2.696667 23.94067 0.248 89.987 65.027 22.51133 16.27833 81.34233 2.177333 110.725 3.139 15.09333 2.330333 1.919333 37.27233 8.791 16.899 7.909333 4.745 11.312 425.357 237.8803 159.4173 18.76 850.6397 16.303 2.154 27.29 51.407 209.5917 18.754 15.92433 87.317 6.812333 13.46667 11.438 29.55 47.036 5.733 18.317 8.043333 225.8327 87.42633 223.9227 3.043 5.630333 19.92833 1.991 2.811 642.0663 9.969333 670.486 691.0767 9.642 6.919333 18.88733 57.46833 25.55733 0.6643333 55.73 16.556 56.797 10.216 26.715 5.557333 103.9153 22.68433 71.78533 26.67967 91.49933 1.911333 24.758 4.766333 27.48633 171.0287 0.7683333 3.468 30.828 37.25567 5.931333 15.01 7.844 17.19067 4.531333 15.18033 29.18933 66.65833 15.73033 21.51767 14.063 6.559667 74.79833 4.156333 22.31233 19.11967 39.67767 24.63167 23.09367 17.96533 64.82733 75.469 4.371 4.59 6.819 10.30533 8.807333 11.227 10.95167 6.455667 3.941333 17.221 30.80767 86.883 5.802333 5.615667 13.08133 759.571 27.59267 27.83967 103.2833 26.75667 22.752 0.485 9.507333 7.039 241.785 6.980333 42.57533 18.30367 6.527333 62.50533 22.93933 8.162667 50.469 11.29367 4.341667 22.17067 393.3037 79.21967 216.0503 6.496333 12.98 27.94767 7.163 28.057 9.735667 15.08833 497.7577 5.177333 39.57833 12.39433 6.674 0 7.412333 49.835 7.107 12.753 13.78833 18.233 2.534667 11.22367 18.62433 47.42233 8.316667 142.0663 20.135 52.084 11.286 26.291 20.37167 37.255 16.40367 5.895 8.497 0.3666667 0 21.116 31.32 44.93767 50.97333 2.592667 443.3597 2.163667 12.36433 6.929 13.65367 20.261 20.74967 20.992 6.300667 7.48 1.469333 35.29633 32.849 8.631333 9.557333 27.23133 28.45833 260.666 321.257 2.900667 23.67567 1.688667 3.857 11.93267 55.59767 8.077 118.9327 44.996 84.312 22.627 30.424 9.613667 19.73 7.354 2.723 20.16567 22.996 1.288 14.94733 7.310333 28.33667 5.364667 19.921 1.162333 33.50367 77.21567 9.824333 7.884667 40.34367 14.78033 8.578333 20.71867 33.01633 9.767333 6.524 4.963667 44.07433 8.002 1.448333 9.773333 15.64 13.22967 11.817 14.06433 10.38333 12.40267 14.22267 0.9146667 18.30633 1.302333 25.32233 18.33267 17.692 4.676 28.43467 8.403667 8.393333 25.40433 17.85933 7.050333 35.802 1.160333 21.69333 3.424 5.558333 15.57933 27.77367 39.729 8.173 5.720333 21.06767 1.715333 14.91467 6.066 9.616 18.94267 25.361 30.75333 13.58 11.59067 7.555333 14.16 10.12033 18.23433 7.216333 8.866333 7.672667 17.332 42.16967 1.252 1.444 11.994 1.363333 6.380333 6.910667 57.61633 12.76533 5.740333 6.248333 2.411 11.758 7.394333 7.431333 8.791667 9.744667 11.097 33.10033 11.36067 44.679 1.992333 13.23767 11.21733 6.863 12.14267 5.603 3.162667 5.332667 18.93367 7.083333 1.695333 5.416333 6.204 5.581333 2.976667 3.762 33.815 2.682667 7.585333 0 3.09 10.85033 20.36133 6.592 21.88733 0 3.979 8.395 25.089 11.89067 8.805333 1.574667 16.06567 13.50467 3.541667 0 2.844 2.605 1.122 5.264 3.109667 6.983667 9.471667 53.09233 2.818 4.926 8.198 10.201 5.596333 2.745 6.861667 6.067667 9.752333 6.752667 3.294667 1.897333 0.4176667 6.521 0.01 2.715 7.621667 12.883 7.766333 21.32033 2.14 5.057 8.293333 7.601333 5.421333 11.40267 4.058 1.981333 0 13.88733 3.292 23.38367 7.325667 8.351333 3.765 6.567 15.09267 7.168667 0.7146667 3.418667 8.889333 1.281667 4.638 12.67933 6.625333 4.064333 1.351667 2.922 0 2.310667 8.038333 0.2473333 4.196 5.686333 6.512667 4.695333 1.769667 18.91833 3.822 8.223667 2.474333 2.517333 4.053 1.851 3.090333 1.407667 1.994667 6.754333 7.337333 161.101 8.255667 0.5473333 0.622 7.195333 1.649667 4.009 1.089 2.883333 1.492667 3.425333 0.9123333 16.116 4.765 8.773 3.273 0.409 4.325333 3.733667 2.194 0.676 5.060667 4.989667 0.939 4.572333 2.800667 3.219333 1.547 3.122667 0 3.696333 6.813333 3.179 36.09 1.576667 0 0.7693333 6.893667 3.493 0 2.414667 2.275333 1.637333 1.980333 4.387 0 3.293333 1.776 12.75533 2.337333 3.403333 11.126 2.877333 1.344 2.663333 3.021333 3.398 2.692333 7.756333 6.45 1.544333 3.077333 2.448333 2.347333 0.4253333 4.451333 2.577667 3.570667 8.963667 3.319667 0.989 3.992 2.259667 3.945667 4.385333 5.633333 2.578333 4.611667 2.573667 2.777667 0 1.844333 2.623333 2.285667 1.56 1.800333 1.305 3.988333 1.324 2.962333 4.123667 8.504333 0.8176667 1.929667 4.52 0 4.080333 5.287333 4.444667 2.242667 0.7723333 1.784333 4.893667 2.252333 2.192 0.604 1.807333 1.697667 0 0.4806667 0 2.396667 3.511333 2.529667 0 1.870667 0.9256667 0 2.706333 0.8176667 1.130667 2.881333 1.452333 1.141667 2.325 0 2.705667 1.002 2.617 6.169 2.246 1.010333 1.322 0 1.383 0.9066667 0 1.125333 1.184333 4.289667 0 0 0 1.916 5.855667 0.67 0 4.041 3.683667 5.097667 0 1.665 0 11.26433 1.733333 2.746333 4.773 2.482667 3.556333 2.415333 14.30567 0 3.535667 3.810667 1.562333 1.461667 0 1.622667 3.218333 1.723 1.277333 1.577333 3.201 2906s sampleB_mean: 2001.57 205.6727 348.3133 1524.761 2415.454 437.971 472.5113 149.84 339.544 736.2793 266.1853 208.1393 1440.661 2830.628 285.4657 2786.993 809.747 370.6363 686.1263 1611.849 1997.885 1889.849 566.031 344.6643 3005.897 856.342 1374.611 4325.944 112.4467 90.55133 105.6647 768.1787 759.8243 161.9667 253.343 2237.994 394.7987 382.0493 317.0973 211.0497 953.5553 118.7197 875.9707 562.3953 4759.337 3179.415 378.7327 556.5843 146.4013 3396.666 574.6353 73.643 177.154 3330.022 144.7763 2471.048 67.006 120.2137 79.82167 3693.07 2047.901 3249.388 136.4467 156.2033 142.302 3216.203 300.4817 476.768 2922.537 267.5577 140.0233 421.1887 2883.64 132.7817 630.4883 240.971 192.3193 2374.126 125.4973 485.2353 130.9923 265.6093 606.0663 151.719 310.312 166.0277 140.997 3620.716 164.205 241.776 4198.375 135.609 255.2837 87.15567 3756.434 140.1517 439.0257 171.3853 279.329 83.61967 68.593 298.0877 141.5657 60.04567 1235.974 105.0843 269.2717 4427.58 760.6557 58.96367 199.6 193.8653 692.2687 167.053 4251.336 165.0047 366.0723 267.723 104.978 341.4467 332.1813 1094.26 5398.857 4895.859 609.5917 2376.446 2990.729 65.65667 87.31133 90.86167 71.08433 120.8233 461.5343 116.6347 165.4787 189.5857 320.243 189.6917 263.798 3709.705 194.996 194.1133 109.1813 3616.512 80.36 731.863 96.602 84.91167 42.12067 166.8767 82.68433 683.449 699.6877 155.4747 177.3257 401.21 81.26567 511.8627 126.504 253.0167 119.8297 59.379 218.6657 97.3 133.069 118.3287 120.4613 177.183 2436.015 925.7747 927.6743 132.628 3423.331 1604.347 39.998 212.3977 321.7517 1034.454 105.6257 133.1023 365.2543 166.5273 143.3147 160.1683 127.811 203.65 96.957 98.13967 303.0437 1012.972 434.556 1049.838 117.851 55.55933 79.65933 80.46333 57.69533 2890.802 58.79033 3849.83 3650.525 90.957 92.061 138.4137 290.862 160.4317 84.001 274.3337 385.176 366.123 195.2947 178.71 38.85333 444.0447 150.3183 280.2643 178.5933 357.7387 72.596 193.4727 79.68 189.0233 878.6043 96.94267 64.25433 175.8867 260.6683 131.585 117.2697 92.43267 132.4173 82.67333 90.116 259.148 287.485 88.38 96.142 75.75133 183.3313 1621.57 87.65567 161.1673 120.8867 254.1857 127.943 216.949 115.1327 255.8583 428.623 51.73767 60.63 85.78933 140.2763 40.32533 240.6073 127.5543 103.81 31.73 123.721 125.2547 404.5893 58.06633 93.48367 91.18133 5152.482 149.819 168.0607 443.3713 213.8997 194.3873 76.24933 109.6237 123.938 1082.98 67.408 162.5713 150.3003 85.55767 382.3843 220.7547 69.18967 286.777 59.23867 76.57167 184.3507 1642.015 496.8353 842.3293 48.27933 74.99667 162.3163 293.9087 218.8733 91.509 62.39367 3067.808 133.338 153.0033 53.59967 59.629 22.75467 136.346 351.08 69.947 134.7907 88.725 107.4287 43.412 74.632 83.573 252.983 67.72533 568.8347 116.5553 224.5063 132.2 199.317 101.0153 229.5497 143.607 61.29533 72.854 36.6 251.767 95.749 148.7563 207.045 232.1147 71.74267 1780.032 423.253 71.93733 49.419 108.7427 140.8457 145.5417 87.012 33.62833 57.40167 68.608 136.5493 151.599 90.91333 96.76 195.6537 186.8647 1395.183 1547.523 32.967 143.433 36.13033 83.324 68.66267 303.08 53.67167 460.2323 231.7267 473.3597 110.8577 124.6713 62.05533 78.48367 41.93 69.599 102.0507 136.4563 30.70733 138.9263 80.51633 174.409 34.301 118.1207 61.53933 143.872 323.664 84.66667 76.68167 161.956 96.91167 77.97333 79.32433 183.9787 45.994 35.42167 47.35667 177.785 48.91 127.1577 67.53533 89.57667 84.28567 53.655 69.52233 71.949 63.03733 71.81167 61.21367 188.329 130.8803 114.4257 88.05067 127.9993 65.56833 188.4637 71.28167 51.723 100.6683 77.092 36.76567 142.4753 28.55333 311.329 34.95467 56.562 78.28033 123.1273 280.2713 50.22033 39.086 90.31267 36.53367 77.38367 57.43267 63.84367 176.0977 98.33933 151.883 126.4583 53.014 29.627 76.47533 55.85733 159.7823 36.70233 53.52367 40.14733 68.32067 178.2697 36.72267 59.38567 120.206 41.03967 79.551 27.296 230.7707 61.12667 38.799 30.21933 22.85467 150.4293 47.69067 51.13867 61.486 68.67667 47.47333 137.8557 76.577 191.3687 30.54067 62.81267 73.193 30.35033 183.6017 186.3597 29.26867 27.176 100.608 27.671 19.45267 37.65433 43.65367 48.22433 31.70567 57.43367 131.6793 27.28933 43.97967 7.787333 37.55767 48.89833 84.57567 48.224 106.615 7.434333 93.36767 42.95633 149.342 106.4977 49.36433 84.23433 84.252 62.27133 33.21433 19.23067 35.499 33.399 27.11633 44.01933 44.45533 37.29667 49.472 356.891 67.063 58.25633 32.39667 55.77667 40.13033 39.59267 79.067 45.60867 42.28633 65.255 14.628 21.83433 19.80633 35.098 18.93767 33.473 31.972 50.84367 52.33733 91.86567 22.669 34.77567 79.87367 31.336 27.93333 50.05667 27.94833 49.82833 86.78467 69.843 33.73067 329.1877 42.60033 58.12767 28.714 33.70267 61.76067 31.52433 73.018 32.58033 34.46367 20.92033 46.144 61.23533 25.97433 30.03567 14.83167 16.267 20.285 31.73667 38.139 19.36667 56.93233 21.914 98.03267 106.1883 27.04033 107.6573 15.205 117.513 33.19833 30.23233 17.84967 13.23833 16.67967 12.861 18.55533 37.849 77.94767 885.105 49.72933 28.44433 17.43 30.596 18.50433 26.188 15.25033 28.15867 20.05633 15.277 24.30433 95.334 34.77033 78.66133 18.09167 18.61167 22.413 70.27367 16.95033 31.89 26.27467 65.14467 23.73133 37.429 22.274 29.242 19.614 15.02733 30.69133 26.23633 27.944 20.35933 166.674 17.502 18.48833 17.31067 28.39433 13.99333 3.268 38.715 17.236 13.41633 12.443 21.34167 31.383 13.36767 35.44867 66.67867 23.945 18.03233 80.966 15.656 13.94367 15.33767 46.892 16.01333 17.96033 38.17233 62.73233 28.76267 28.101 39.09833 12.703 13.18233 32.61467 17.898 16.27233 62.61533 14.817 29.174 16.55367 13.60433 35.23233 18.28267 41.99133 15.10167 22.38467 20.55233 19.04733 23.57 14.40533 17.09767 20.926 15.269 20.43233 10.317 15.90267 11.96033 20.87567 22.969 37.68333 21.75 21.75767 29.889 14.14033 22.439 25.09 22.49467 17.53033 21.54967 11.87167 26.32667 19.42067 12.63367 15.508 9.565333 11.406 26.512 13.284 25.41533 22.467 14.73 17.607 20.102 48.44967 13.124 12.082 32.57833 16.799 13.01133 17.52867 10.03867 22.88133 16.668 40.46467 13.56067 19.44067 18.108 29.66167 9.561333 12.414 14.34133 7.422 11.82467 16.34867 17.859 11.65033 13.48967 23.23533 3.817667 15.03767 18.481 14.066 38.401 11.25967 3.536 29.10133 17.881 25.72733 32.58667 11.77733 3.745333 78.33933 13.629 26.44433 20.93267 24.97333 15.16033 10.763 72.94233 12.603 16.31933 42.748 25.30367 15.533 4.657333 15.84367 17.09167 16.32567 8.590333 25.56867 19.31367 2906s num discordant: 0 2906s validating: Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset 2906s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test. 2906s sampleA_mean: 322.6313 2373.043 328.0923 2550.414 768.306 12470.43 620.017 510.9113 1781.496 440.9727 3211.031 514.415 224.469 876.8277 95.89333 4624.974 1636.976 512.042 198.0453 177.0987 1506.715 621.286 707.8263 339.8283 411.447 871.6373 646.6133 1101.219 324.8553 1098.868 645.4617 217.5877 493.2167 834.608 347.4017 850.5097 189.5647 501.203 222.09 429.5973 244.213 173.88 615.4837 1003.238 1192.947 306.1523 474.0487 1494.298 565.0517 3078.184 689.711 374.99 856.7063 204.598 900.1817 623.5437 237.177 166.336 378.627 646.864 211.7417 132.9247 198.031 578.1793 257.3087 97.24867 109.0163 88.61667 194.2893 151.8027 661.7387 138.8203 75.79967 153.4527 116.0807 189.876 149.5763 194.0203 188.654 112.6127 272.869 506.512 499.6263 276.1017 103.6453 92.354 189.338 215.8967 202.739 175.2467 63.519 160.284 278.7853 53.598 37.50533 2633.716 161.0497 103.0963 91.645 100.247 374.3023 131.159 54.95833 112.168 72.98133 214.853 59.07767 583.86 39.40267 55.41567 46.03533 45.62033 63.24267 114.2777 94.455 55.17567 80.30267 106.367 51.208 82.208 58.90833 36.49633 31.404 66.74667 103.33 50.66867 43.62667 541.9867 13.208 29.69867 99.289 30.70067 72.57967 46.59433 69.91033 170.258 83.27833 50.351 39.44033 41.25767 52.59533 75.16967 42.52533 28.455 227.2843 39.745 82.00433 40.44433 33.46233 137.7607 28.618 35.30367 32.245 63.80367 24.83067 134.6853 38.06967 75.28167 43.80133 18.93167 7.618667 25.087 40.18733 124.9103 25.539 48.025 92.552 36.466 27.874 81.69967 19.68333 68.14433 29.06367 25.74867 72.777 63.05533 57.61033 37.18267 58.47233 22.32333 20.62167 79.93733 50.767 59.28433 22.33433 76.51933 43.573 55.27767 28.191 31.40267 24.891 19.09633 63.71067 27.69933 23.51433 116.5107 78.60667 48.16367 48.78233 67.73133 23.021 147.841 45.16833 29.71933 31.779 52.69467 69.305 31.79067 122.654 62.14133 26.44133 31.89567 27.838 18.868 36.90167 56.21533 19.622 23.01233 32.10933 23.8 26.81733 23.75833 101.7453 49.08533 33.90867 18.83133 57.80667 28.387 45.292 72.11233 24.45867 39.1 19.95933 22.708 35.719 23.05967 64.09967 93.41733 11.958 64.68467 48.198 58.21167 19.54733 14.43033 13.03933 41.316 22.16333 37.25433 22.77433 22.89067 21.97633 28.69233 43.359 14.56467 23.558 37.281 44.44267 25.653 45.90233 27.504 23.64233 17.79667 26.64367 36.46133 10.555 40.67867 24.61133 70.339 13.487 28.572 34.59267 45.92167 133.2117 16.99367 37.914 24.47467 28.30367 33.908 23.85167 30.64067 62.26333 21.27433 34.511 22.96933 17.955 51.61667 23.06333 32.872 18.41033 11.50733 44.84 5.414333 9.291 15.83533 19.36833 16.25467 38.27767 11.65967 33.81667 15.14 30.82967 15.25267 20.10433 21.40767 29.75367 28.19233 22.45533 16.872 17.03133 18.279 29.146 20.381 6.829667 18.92167 17.45867 19.253 35.64 15.35867 42.82367 2906s sampleB_mean: 0 8.807333 1.413333 16.70467 11.541 312.258 19.323 17.62467 78.223 21.142 176.0093 28.83167 15.272 59.789 6.833333 341.9077 131.954 41.31433 17.10933 18.75567 165.372 70.838 84.293 40.62 51.37267 107.8423 84.69133 143.015 42.12067 162.736 98.93967 33.19 77.04167 149.042 72.11933 173.185 21.17867 107.4767 40.211 60.698 24.36067 11.974 3.97 231.01 230.7603 60.63 62.01667 361.5717 3.203 644.6073 91.85267 63.14733 147.5103 31.336 190.2367 149.0183 52.02367 8.328333 50.806 126.507 47.04433 22.66633 35.05467 5.375333 52.632 20.43633 14.771 4.436 15.897 21.67633 126.2827 21.66667 14.72967 22.414 23.35133 43.86567 30.432 27.23467 25.96333 3.546 61.038 113.391 52.72333 49.04333 13.34567 11.42567 5.980333 43.19967 35.93933 36.80733 4.816667 5.957333 38.81867 7.705667 6.593 603.3247 34.63 15.84233 15.47833 21.97267 84.23433 21.75133 11.08667 20.231 15.958 47.94933 13.23833 126.723 1.620333 11.73133 3.929667 6.119333 6.474667 24.79367 7.766333 5.855333 15.00967 21.74967 7.976 14.15433 7.353333 2.201333 7.205333 15.63733 21.066 0.6883333 4.916 101.151 0 1.439333 22.53 6.552 1.932 6.709 4.875667 21.36367 8.861667 2.48 4.478333 3.745333 10.64267 15.06367 0 3.039667 53.09067 7.033333 0 7.920333 2.116667 34.28533 3.831 3.374 6.818 14.63867 1.628667 12.223 3.003333 7.897667 5.966667 1.101667 0 5.451 6.937333 21.018 4.024 4.954667 8.839667 6.506333 6.301667 19.603 3.384 1.799 1.569 3.431333 14.62267 5.157 6.500333 8.477667 8.693333 1.63 1.082 14.45 10.157 5.139 1.765 8.006333 2.462333 3.485333 2.819 6.082333 2.909667 0.4836667 10.28 0.692 5.055333 0.08 0.05333333 7.749 10.15367 5.873 2.511 41.35533 9.145 2.893333 1.487333 5.417 13.05267 7.386333 19.24567 9.771667 4.422333 6.758333 0.8023333 2.849667 8.017333 12.1 2.936333 4.993333 2.181667 2.193667 5.261333 0 25.41533 5.657333 2.136333 4.229333 2.217667 4.762667 10.16333 16.907 1.362 4.943333 3.54 4.677 3.098 4.158333 9.295333 14.763 2.343667 10.456 8.646 12.014 0 1.481667 0 3.833667 0.8846667 6.111 2.732667 3.947333 2.95 6.918667 5.704667 2.289 4.627333 1.766333 6.405333 5.972667 2.344 3.367 3.727667 3.412667 3.223333 8.528 2.445 2.058 2.001 16.79133 1.764667 5.310333 5.351 10.56633 31.983 2.097 8.735 0 3.839 1.942 4.567333 7.471 16.31167 3.862 1.925667 0 2.384 7.252 5.472667 3.237667 0.911 2.312667 4.294667 0 0 2.121667 0 1.519333 8.592 2.345 2.112667 2.622333 1.783333 3.487 0 3.301 1.833667 4.401 2.345 0 1.633667 1.173667 0 0 0.3683333 3.405667 3.381 4.706333 6.860333 1.718 10.319 2906s num discordant: 0 2906s File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test. 2906s validating: Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset 2906s sampleA_mean: 4.98 16.50567 117.2063 112.322 62.58133 37.23367 40.96933 28.62567 210.276 110.7323 73.97767 77.55333 94.08633 56.147 95.99433 311.829 220.5287 24.33867 534.2237 138.353 191.8153 105.9497 53.11833 658.8357 135.901 407.2907 1020.23 773.7893 825.1763 59.968 124.4243 55.75367 501.0717 2661.226 0 65.965 30.499 81.05967 36.99433 53.687 88.495 36.84367 50.429 189.9813 132.8633 62.68467 21.54267 12.544 2.172 83.305 12.42267 180.8457 53.33433 17.029 341.9023 58.24233 14.554 25.096 104.7537 48.72833 42.797 47.89667 57.313 3.969667 49.103 193.8337 9.165333 3.122 17.875 39.58367 68.49367 17.60767 15.418 54.28 115.6623 6.042667 56.695 9.605 24.273 16.69733 21.25867 42.71533 19.86033 39.777 133.0233 336.3973 30.00467 35.78433 7.538 11.277 23.53367 41.80933 15.26033 199.8083 5.607667 16.22733 7.374 22.84267 8.516333 63.41767 21.14433 342.208 41.83033 40.53433 3.966667 10.63267 24.02367 103.5143 20.959 31.04633 25.39133 32.75133 41.856 23.71433 14.411 35.43333 5.832 57.13467 24.38833 14.56933 29.33233 24.772 36.41067 7.960667 45.89833 28.28467 5.097667 70.13033 12.85033 29.44033 12.023 22.77967 6.926 8.362 15.28167 13.52433 16.53733 31.838 10.23233 8.268 91.47333 40.92067 12.36 75.059 6.981333 25.25367 31.61067 56.92767 7.083 15.559 21.88967 238.9387 15.914 12.771 21.31667 16.38067 6.314 88.60033 43.318 2.792667 2.752667 17.12667 10.30967 20.27767 40.359 7.979667 23.029 8.47 10.16833 5.342333 10.49233 7.825667 21.02533 65.86733 5.777667 49.53233 12.81233 8.79 11.38633 12.13567 18.746 21.765 28.07033 5.772333 11.90333 9.187667 7.526667 27.34567 21.686 5.664333 2.727 19.21233 5.464 6.437333 5.960667 18.06167 2.539333 3.51 15.31167 46.84667 64.78933 3.596 16.75833 35.59733 37.02633 54.65067 5.197667 12.438 4.820333 21.776 17.25667 20.79733 22.86533 3.046667 24.662 7.951 22.029 32.918 7.603667 14.33467 16.17933 11.03933 6.225667 14.50533 23.46733 8.792667 7.807333 29.746 6.306667 11.28667 8.809 10.73033 3.531333 8.48 0.8883333 22.12067 6.174667 14.356 7.113667 5.639333 74.98367 7.839333 3.158 0 5.134333 0 6.934 3.201 12.918 78.08667 1.752333 5.177333 7.395 7.025 1.506333 19.07367 0 9.925 3.503 3.788 13.76033 7.259 5.081 8.591 23.97033 10.31933 9.197667 0 7.501667 7.014667 2.654667 2.409667 3.867 2.723333 8.232 4.912333 6.318 2.349 1.934333 0.2506667 6.052333 23.34367 3.773667 0.093 2.518667 0.5686667 2.742667 3.633333 7.901333 5.981333 2.414667 2.105667 2.653333 7.077333 2.888 2.993667 6.688 4.237 10.41 7.560667 1.734 9.876 9.321667 2.503 4.064667 5.407667 2.677333 3.311333 0 4.158 19.63133 6.958667 3.617 7.296333 1.742333 0.4486667 0 2.967333 8.351 10.97667 4.931333 2.231667 3.471667 7.922333 3.082 1.651333 2.362667 10.806 5.76 6.261 3.945333 3.743 3.012 2.387667 2.98 1.755667 4.701 1.848333 2.767667 19.41933 1.224333 2.625667 0 1.870667 0.4626667 0 1.403333 1.814333 4.514333 0 5.397667 13.32033 2.961333 2.188333 3.138333 4.864 7.176667 0 3.174667 5.445 1.803333 1.448333 1.584 12.06 2.361 2.965333 2.893667 0.829 1.168333 2.242 3.214 8.255667 7.399 4.021333 1.874 3.013 5.335333 1.322667 1.187667 2.536333 2.772 4.765 0.733 0.5746667 2.15 2906s sampleB_mean: 1440.661 584.575 3506.467 2786.993 843.2847 461.5343 501.3557 317.4807 2415.454 1202.982 805.275 809.747 968.2863 562.3953 878.6043 2830.628 2047.901 203.078 4004.8 953.5553File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test. 2906s 1242.884 686.1263 339.544 4216.251 807.5603 2355.907 5398.857 3709.705 3756.434 266.1853 513.784 222.0223 2001.57 13329.63 174.965 317.8843 378.7327 786.1327 279.329 256.6427 574.6353 208.1393 573.2667 926.6357 641.6557 303.08 255.2837 137.7833 58.96367 401.8723 166.8767 1012.972 371.2327 286.777 1524.761 310.312 148.789 166.0277 468.317 224.5063 255.0223 265.6093 255.8583 59.23867 290.862 731.863 177.154 91.739 116.6347 320.243 585.796 156.2033 194.1133 205.6727 720.0863 90.957 387.0143 109.3147 145.604 151.719 168.2893 263.0527 121.5623 157.5777 1082.98 1576.856 125.2547 178.71 303.0437 110.8993 132.4173 158.383 124.6713 1109.48 99.863 194.3873 143.872 301.9357 127.5543 477.213 213.8997 1834.421 195.216 682.0817 102.0507 92.061 150.3003 496.8353 143.3147 163.1987 156.0383 219.6953 278.7393 120.8867 179.874 160.5167 91.509 232.1147 148.7563 91.18133 161.1673 163.021 148.6807 98.33933 178.2697 145.137 87.65567 311.44 70.221 151.599 96.804 918.9367 41.78967 51.73767 143.0897 57.44367 119.8297 263.5397 69.18967 67.408 405.776 161.4237 101.4477 332.2983 31.73 174.6973 160.1683 253.0167 64.25433 108.837 109.0193 4759.337 117.851 118.1207 83.61967 109.6677 71.81167 437.7257 193.3587 76.24933 29.627 85.78933 53.655 138.9263 188.56 192.615 113.004 96.91167 46.842 24.80467 48.96533 60.90233 293.9087 285.3807 251.767 195.2947 96.94267 41.93 64.15933 84.001 82.68433 141.0183 126.6913 51.723 63.62167 54.097 71.949 174.409 141.442 47.31267 36.6 107.2877 36.76567 56.05633 50.22033 91.49033 32.39667 37.96133 130.4127 216.4093 250.7013 27.192 76.82 136.4563 191.0543 230.7707 27.296 311.329 68.67667 90.427 317.6723 125.7047 97.60633 29.675 176.0977 44.69833 127.9993 170.7463 127.1577 106.615 93.09033 68.608 61.53933 216.4057 169.1617 44.98367 29.00467 120.0493 41.517 84.252 49.09733 55.476 36.53367 39.086 19.95267 112.8043 28.425 73.193 61.76067 59.38567 381.953 34.05967 30.93667 24.882 40.13033 19.80633 43.94933 31.46 52.36933 356.891 33.473 30.54067 28.775 58.12767 18.20933 75.443 18.23433 41.50267 20.82433 24.244 76.899 27.29533 54.54667 65.255 106.4977 48.14767 61.80233 6.507333 31.52433 27.23833 28.39433 16.15667 30.03567 31.73667 42.92033 33.73067 129.8027 86.78467 28.30833 19.36667 27.607 93.36633 24.241 12.004 26.27467 18.004 22.782 19.99067 34.77567 24.384 20.92033 28.15867 33.19833 28.714 23.60467 15.938 68.356 15.87267 40.12533 32.58033 19.23067 49.72933 44.13267 11.60833 27.04033 21.00233 72.35433 18.612 3.268 20.046 178.6527 80.966 18.62033 33.75167 38.715 16.761 31.383 12.202 54.89133 73.018 20.212 17.502 14.948 70.27367 31.89 27.84133 17.43 68.52333 28.421 25.473 20.05633 15.33767 35.44867 30.69133 16.92567 16.162 18.50433 15.13667 17.09767 183.9787 17.607 19.71067 15.228 19.42067 4.691 14.14033 18.108 17.881 23.30167 20.102 21.03667 65.14467 45.46433 14.85333 14.73 20.91 32.61467 26.512 12.84233 23.73133 11.96033 11.83367 11.77833 62.73233 13.698 13.354 21.75767 16.799 13.01133 10.317 13.157 42.515 39.66833 17.93933 10.60267 16.80767 26.071 24.89367 22.072 15.71033 15.253 23.78967 11.25967 9.569333 14.066 2906s num discordant: 0 2906s touch test_edgeR 2906s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method DESeq2 -s samples.txt -o DESeq2_outdir 2906s Got 9 samples, and got: 10 data fields. 2906s Header: wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 2906s Next: TR24|c0_g1_i1 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00 2906s 2906s $VAR1 = { 2906s 'wt_37_1' => 3, 2906s 'wt_GSNO_3' => 4, 2906s 'wt_ph8_1' => 8, 2906s 'wt_ph8_3' => 7, 2906s 'wt_GSNO_2' => 6, 2906s 'wt_GSNO_1' => 5, 2906s 'wt_37_2' => 1, 2906s 'wt_37_3' => 2, 2906s 'wt_ph8_2' => 9 2906s }; 2906s $VAR1 = { 2906s 'wt_37' => [ 2906s 'wt_37_1', 2906s 'wt_37_2', 2906s 'wt_37_3' 2906s ], 2906s 'wt_GSNO' => [ 2906s 'wt_GSNO_1', 2906s 'wt_GSNO_2', 2906s 'wt_GSNO_3' 2906s ], 2906s 'wt_ph8' => [ 2906s 'wt_ph8_1', 2906s 'wt_ph8_2', 2906s 'wt_ph8_3' 2906s ] 2906s }; 2906s Contrasts to perform are: $VAR1 = [ 2906s [ 2906s 'wt_37', 2906s 'wt_GSNO' 2906s ], 2906s [ 2906s 'wt_37', 2906s 'wt_ph8' 2906s ], 2906s [ 2906s 'wt_GSNO', 2906s 'wt_ph8' 2906s ] 2906s ]; 2906s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.Rscript 2906s Loading required package: edgeR 2906s Loading required package: limma 2907s Loading required package: DESeq2 2907s Loading required package: S4Vectors 2907s Loading required package: stats4 2907s Loading required package: BiocGenerics 2907s 2907s Attaching package: ‘BiocGenerics’ 2907s 2907s The following object is masked from ‘package:limma’: 2907s 2907s plotMA 2907s 2907s The following objects are masked from ‘package:stats’: 2907s 2907s IQR, mad, sd, var, xtabs 2907s 2907s The following objects are masked from ‘package:base’: 2907s 2907s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 2907s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 2907s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 2907s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 2907s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 2907s tapply, union, unique, unsplit, which.max, which.min 2907s 2908s 2908s Attaching package: ‘S4Vectors’ 2908s 2908s The following object is masked from ‘package:utils’: 2908s 2908s findMatches 2908s 2908s The following objects are masked from ‘package:base’: 2908s 2908s expand.grid, I, unname 2908s 2908s Loading required package: IRanges 2909s Loading required package: GenomicRanges 2909s Loading required package: GenomeInfoDb 2910s Loading required package: SummarizedExperiment 2910s Loading required package: MatrixGenerics 2910s Loading required package: matrixStats 2910s 2910s Attaching package: ‘MatrixGenerics’ 2910s 2910s The following objects are masked from ‘package:matrixStats’: 2910s 2910s colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, 2910s colCounts, colCummaxs, colCummins, colCumprods, colCumsums, 2910s colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, 2910s colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, 2910s colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, 2910s colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, 2910s colWeightedMeans, colWeightedMedians, colWeightedSds, 2910s colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, 2910s rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, 2910s rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, 2910s rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, 2910s rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, 2910s rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, 2910s rowWeightedMads, rowWeightedMeans, rowWeightedMedians, 2910s rowWeightedSds, rowWeightedVars 2910s 2910s Loading required package: Biobase 2910s Welcome to Bioconductor 2910s 2910s Vignettes contain introductory material; view with 2910s 'browseVignettes()'. To cite Bioconductor, see 2910s 'citation("Biobase")', and for packages 'citation("pkgname")'. 2910s 2910s 2910s Attaching package: ‘Biobase’ 2910s 2910s The following object is masked from ‘package:MatrixGenerics’: 2910s 2910s rowMedians 2910s 2910s The following objects are masked from ‘package:matrixStats’: 2910s 2910s anyMissing, rowMedians 2910s 2915s converting counts to integer mode 2916s estimating size factors 2916s estimating dispersions 2916s gene-wise dispersion estimates 2917s mean-dispersion relationship 2917s final dispersion estimates 2917s fitting model and testing 2920s null device 2920s 1 2920s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.Rscript 2921s Loading required package: edgeR 2921s Loading required package: limma 2921s Loading required package: DESeq2 2921s Loading required package: S4Vectors 2921s Loading required package: stats4 2921s Loading required package: BiocGenerics 2921s 2921s Attaching package: ‘BiocGenerics’ 2921s 2921s The following object is masked from ‘package:limma’: 2921s 2921s plotMA 2921s 2921s The following objects are masked from ‘package:stats’: 2921s 2921s IQR, mad, sd, var, xtabs 2921s 2921s The following objects are masked from ‘package:base’: 2921s 2921s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 2921s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 2921s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 2921s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 2921s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 2921s tapply, union, unique, unsplit, which.max, which.min 2921s 2922s 2922s Attaching package: ‘S4Vectors’ 2922s 2922s The following object is masked from ‘package:utils’: 2922s 2922s findMatches 2922s 2922s The following objects are masked from ‘package:base’: 2922s 2922s expand.grid, I, unname 2922s 2922s Loading required package: IRanges 2923s Loading required package: GenomicRanges 2923s Loading required package: GenomeInfoDb 2924s Loading required package: SummarizedExperiment 2924s Loading required package: MatrixGenerics 2924s Loading required package: matrixStats 2924s 2924s Attaching package: ‘MatrixGenerics’ 2924s 2924s The following objects are masked from ‘package:matrixStats’: 2924s 2924s colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, 2924s colCounts, colCummaxs, colCummins, colCumprods, colCumsums, 2924s colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, 2924s colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, 2924s colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, 2924s colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, 2924s colWeightedMeans, colWeightedMedians, colWeightedSds, 2924s colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, 2924s rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, 2924s rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, 2924s rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, 2924s rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, 2924s rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, 2924s rowWeightedMads, rowWeightedMeans, rowWeightedMedians, 2924s rowWeightedSds, rowWeightedVars 2924s 2924s Loading required package: Biobase 2924s Welcome to Bioconductor 2924s 2924s Vignettes contain introductory material; view with 2924s 'browseVignettes()'. To cite Bioconductor, see 2924s 'citation("Biobase")', and for packages 'citation("pkgname")'. 2924s 2924s 2924s Attaching package: ‘Biobase’ 2924s 2924s The following object is masked from ‘package:MatrixGenerics’: 2924s 2924s rowMedians 2924s 2924s The following objects are masked from ‘package:matrixStats’: 2924s 2924s anyMissing, rowMedians 2924s 2929s converting counts to integer mode 2929s estimating size factors 2929s estimating dispersions 2930s gene-wise dispersion estimates 2930s mean-dispersion relationship 2930s final dispersion estimates 2931s fitting model and testing 2934s null device 2934s 1 2934s CMD: Rscript Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.Rscript 2934s Loading required package: edgeR 2934s Loading required package: limma 2935s Loading required package: DESeq2 2935s Loading required package: S4Vectors 2935s Loading required package: stats4 2935s Loading required package: BiocGenerics 2935s 2935s Attaching package: ‘BiocGenerics’ 2935s 2935s The following object is masked from ‘package:limma’: 2935s 2935s plotMA 2935s 2935s The following objects are masked from ‘package:stats’: 2935s 2935s IQR, mad, sd, var, xtabs 2935s 2935s The following objects are masked from ‘package:base’: 2935s 2935s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 2935s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 2935s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 2935s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 2935s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 2935s tapply, union, unique, unsplit, which.max, which.min 2935s 2936s 2936s Attaching package: ‘S4Vectors’ 2936s 2936s The following object is masked from ‘package:utils’: 2936s 2936s findMatches 2936s 2936s The following objects are masked from ‘package:base’: 2936s 2936s expand.grid, I, unname 2936s 2936s Loading required package: IRanges 2937s Loading required package: GenomicRanges 2937s Loading required package: GenomeInfoDb 2937s Loading required package: SummarizedExperiment 2937s Loading required package: MatrixGenerics 2937s Loading required package: matrixStats 2937s 2937s Attaching package: ‘MatrixGenerics’ 2937s 2937s The following objects are masked from ‘package:matrixStats’: 2937s 2937s colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, 2937s colCounts, colCummaxs, colCummins, colCumprods, colCumsums, 2937s colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, 2937s colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, 2937s colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, 2937s colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, 2937s colWeightedMeans, colWeightedMedians, colWeightedSds, 2937s colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, 2937s rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, 2937s rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, 2937s rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, 2937s rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, 2937s rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, 2937s rowWeightedMads, rowWeightedMeans, rowWeightedMedians, 2937s rowWeightedSds, rowWeightedVars 2937s 2937s Loading required package: Biobase 2938s Welcome to Bioconductor 2938s 2938s Vignettes contain introductory material; view with 2938s 'browseVignettes()'. To cite Bioconductor, see 2938s 'citation("Biobase")', and for packages 'citation("pkgname")'. 2938s 2938s 2938s Attaching package: ‘Biobase’ 2938s 2938s The following object is masked from ‘package:MatrixGenerics’: 2938s 2938s rowMedians 2938s 2938s The following objects are masked from ‘package:matrixStats’: 2938s 2938s anyMissing, rowMedians 2938s 2943s converting counts to integer mode 2943s estimating size factors 2944s estimating dispersions 2944s gene-wise dispersion estimates 2944s mean-dispersion relationship 2945s final dispersion estimates 2945s fitting model and testing 2948s null device 2948s 1 2948s cd DESeq2_outdir && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl \ 2948s --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt --order_columns_by_samples_file && \ 2948s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt 2948s 2948s 2948s ** Found 1783 features as differentially expressed. 2948s 2948s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR -m diffExpr.P0.001_C2.matrix --log2 --heatmap --min_colSums 0 --min_rowSums 0 --gene_dist euclidean --sample_dist euclidean --sample_cor_matrix --center_rows --save -s ../samples.txt --order_columns_by_samples_file --sample_clust none 2948s CMD: Rscript diffExpr.P0.001_C2.matrix.R 2949s Loading required package: BiocGenerics 2949s 2949s Attaching package: ‘BiocGenerics’ 2949s 2949s The following objects are masked from ‘package:stats’: 2949s 2949s IQR, mad, sd, var, xtabs 2949s 2949s The following objects are masked from ‘package:base’: 2949s 2949s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 2949s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 2949s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 2949s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 2949s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 2949s tapply, union, unique, unsplit, which.max, which.min 2949s 2949s Welcome to Bioconductor 2949s 2949s Vignettes contain introductory material; view with 2949s 'browseVignettes()'. To cite Bioconductor, see 2949s 'citation("Biobase")', and for packages 'citation("pkgname")'. 2949s 2950s [1] "Reading matrix file." 2950s 2950s Attaching package: ‘fastcluster’ 2950s 2950s The following object is masked from ‘package:stats’: 2950s 2950s hclust 2950s 2950s for plotting:: min.raw: -0.674993513119273 max.raw: 1 2950s null device 2950s 1 2950s Warning messages: 2950s 1: In heatmap.3(sample_cor_for_plot, dendrogram = "both", Rowv = RowV, : 2950s Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram. 2950s 2: In heatmap.3(sample_cor_for_plot, dendrogram = "both", Rowv = RowV, : 2950s Discrepancy: Colv is FALSE, while dendrogram is `none'. Omitting column dendogram. 2951s for plotting:: min.raw: -7.50284849776958 max.raw: 7.50284849776958 2951s null device 2951s 1 2953s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset 2953s sampleA_mean: 4954.434 1326.5 1046.9 470.179 1833.283 1037.645 5637.134 1407.266 1371.045 1262.588 982.539 11423.35 1681.385 6030.232 1816.62 335.7477 2191.464 20787.35 1013.064 4776.171 15024.4 522.8673 838.8547 2460.887 3549.085 887.2083 559.8297 484.398 499.8527 4784.861 1120.621 620.238 1445.705 2059.192 562.1487 533.844 5797.692 810.3883 502.9777 1707.219 4182.673 1532.142 637.4673 2891.881 1718.763 581.2863 545.5957 333.5833 4713.887 1066.12 647.4437 772.306 363.4713 480.5827 400.0377 923.62 1512.754 252.8977 1272.664 2616.495 5395.606 2602.336 3468.578 2442.782 4913.275 296.1627 1326.869 567.2883 1229.376 409.7437 198.9307 1939.628 665.289 1265.232 1088.069 1315.006 335.2157 1640.267 373.2207 1291.39 244.753 604.7417 742.0153 508.1423 350.3023 579.459 876.645 301.1237 629 872.2057 1319.258 941.4197 1753.538 323.5933 338.9207 323.2733 425.4187 2635.243 350.1547 180.1727 2002.536 530.7697 182.1447 1099.802 490.2657 134.168 564.1773 574.8767 203.246 912.636 494.789 933.0403 762.2617 482.3557 407.805 579.619 249.8873 198.8237 298.6353 178.6107 210.486 2688.784 599.1197 2207.998 231.4073 731.256 388.648 310.3963 744.858 711.3287 676.234 393.785 104.2153 335.4993 335.637 1125.723 148.374 854.0897 207.4947 584.709 219.039 435.0017 85.82433 127.1483 211.844 481.5627 209.749 914.4587 719.3537 241.211 162.433 150.8137 218.991 322.1607 991.437 122.234 300.3533 419.6373 1214.03 693.0703 1412.697 2446.14 197.342 583.6803 330.6623 387.8127 122.4237 114.123 99.45067 6660.051 1815.027 262.1497 201.4867 356.783 571.859 1547.728 124.028 134.0677 340.5557 323.746 510.4197 456.1583 177.4467 310.3323 617.054 354.781 505.6607 339.0793 167.1063 781.6647 97.82467 2465.916 199.325 446.9747 122.591 136.2463 356.3497 455.3783 192.5983 234.695 256.9907 272.6143 294.269 243.326 690.4453 221.959 172.982 154.4447 563.9263 119.932 183.172 112.757 432.0453 216.15 303.8613 71.71033 594.819 352.3153 156.591 189.715 161.9753 114.485 176.9843 318.1197 240.267 220.177 322.742 369.791 721.5107 342.712 210.2437 152.1197 111.007 783.8573 2952.358 371.817 196.6567 160.8853 313.843 62.65367 80.98433 146.7767 60.22767 328.3217 334.935 123.246 110.791 207.939 334.361 252.697 89.249 407.6713 320.023 169.0567 421.348 156.8307 118.5347 239.7997 86.67367 144.7257 168.189 133.1057 112.5293 62.56033 109.0817 306.508 250.2393 135.433 442.0453 307.9013 69.89367 228.911 99.03533 134.6873 94.07567 75.336 83.207 324.5383 115.132 78.31633 83.07667 172.4453 79.282 79.07433 354.898 1557.898 67.469 42.552 87.49733 160.1673 363.302 4534.064 207.397 299.966 122.177 1606.153 104.0613 93.672 81.80933 97.23167 52.74467 86.386 110.5993 703.739 57.64267 91.61633 55.68233 76.27033 155.7297 280.7067 105.6967 158.1847 398.1303 58.232 526.9727 94.133 603.3643 59.60267 85.95367 114.563 361.8817 164.921 67.206 78.67633 87.15633 31.766 73.085 108.859 100.0123 94.69467 3561.451 33.26767 32.351 1172.149 112.884 91.79433 76.09067 84.972 280.1693 93.57967 84.25 551.5827 64.34933 39.99867 41.339 84.98533 340.941 98.302 31.38733 74.26433 44.71033 47.17133 38.966 37.59833 279.711 246.2103 66.88467 77.01533 80.43867 197.0237 73.806 69.21367 69.92267 64.40333 84.101 46.65767 405.356 69.72667 204.481 306.441 35.384 31.01767 62.81 47.40267 38.21567 144.1087 89.883 103.086 51.06833 56.34967 112.7063 30.17067 32 26.93367 37.93767 40.988 37.304 38.01367 34.95267 67.623 44.67767 95.708 176.214 58.726 38.414 39.204 21.82767 31.13533 53.25667 20.93567 52.91967 32.60533 51.916 422.5397 85.27667 66.12467 49.19267 43.95233 56.22233 30.96067 78.667 71.85 74.20533 32.07433 16.46033 131.435 65.34533 56.78633 171.2653 47.775 27.49133 64.515 158.4163 54.81767 52.662 50.27133 23.42167 40.022 9.429667 69.90667 38.41333 29.75167 115.2073 24.04867 5495.505 23.232 35.23567 89.08767 163.5027 15.402 168.4167 71.55767 84.52867 31.93633 33.50367 52.49167 38.44933 14.64167 34.237 28.112 10.73367 209.263 42.42 8.473333 15.47467 36.76933 41.489 88.74833 20.16567 56.72833 24.90267 40.90567 16.558 20.61433 43.001 36.44033 40.95667 22.18367 14.82667 23.62733 14.972 19.56433 21.19933 23.66867 16.59667 66.32833 67.70667 16.92233 26.74467 9.629333 23.34767 68.59733 32.359 2953s sampleB_mean: 175.7007 98.97567 27.41467 10.76867 63.97333 47.461 68.49367 33.63533 28.87167 9.133333 33.35533 534.2237 10.849 173.6673 3.202333 21.376 98.61433 336.3973 18.23967 543.417 661.7387 28.62567 39.777 73.97767 84.42267 55.41567 32.483 24.33867 18.18567 299.0663 43.62667 12.49967 139.4193 313.6673 52.09567 47.52733 900.1817 63.963 9.088 218.998 658.8357 225.2773 2.778333 125.8543 296.743 27.60133 72.053 36.39433 338.805 183.983 49.48767 68.979 12.30667 39.797 24.273 79.21633 281.149 15.51133 217.05 629.0693 4.127667 514.415 457.8803 563.4113 1003.238 8.580333 191.8153 23.51433 124.0153 42.68733 5.223667 297.3653 12.67333 250.9827 145.798 131.764 43.422 280.8763 53.687 194.2893 5.388667 95.47967 62.58133 79.409 19.23033 102.7107 94.216 55.75367 94.08633 116.6427 117.2063 232.083 375.202 38.47567 50.10333 25.39133 72.874 623.5437 36.41067 27.94467 429.5973 110.7323 18.134 170.561 44.471 13.52433 68.27467 56.695 32.93 115.6623 58.90833 143.4493 43.57767 70.27367 58.22233 113.0753 36.231 22.41533 26.58267 32.70533 32.109 462.724 130.483 412.998 7.825667 170.8453 85.85133 29.69867 132.8633 118.5947 116.0857 68.88567 14.398 2.287 74.29867 261.706 9.605 11.05733 28.87667 122.476 9.034667 66.97833 10.49667 14.087 29.54433 105.7627 15.964 213.755 119.1803 22.455 11.277 10.44 48.99067 6.660667 223.4383 10.49233 29.063 50.429 230.2087 150.937 4.412333 582.8023 29.96067 85.73633 43.27 89.28567 3.616 2.461333 10.675 938.454 402.3693 40.96933 23.402 68.36967 87.39733 377.1183 15.837 23.18133 72.46567 38.353 126.7297 80.21667 21.00533 21.807 115.9157 80.928 118.5987 70.59233 33.283 4.512667 10.31967 7.979667 20.14333 88.46167 8.546333 14.554 58.833 92.838 26.01033 45.62033 62.40367 38.81867 55.04367 43.417 154.972 45.02367 6.052333 37.50533 120.0037 22.87333 26.18 12.85033 70.388 45.433 49.50333 10.603 131.159 56.458 30.82233 31.15267 35.82667 2.967333 39.035 73.76233 44.52567 16.50567 73.756 70.13033 80.658 71.40267 28.455 26.68733 11.71333 170.3357 424.5863 78.80367 42.91667 14.26033 74.91 4.263 15.42567 32.132 12.03667 43.231 64.78933 29.317 26.685 51.52233 72.094 52.69567 1.321667 96.276 71.137 14.82467 75.955 2.732333 28.90033 41.856 17.759 29.59733 28.625 24.22767 15.32067 11.399 19.12733 71.361 48.89067 15.437 40.53433 65.235 8.867667 40.359 19.23 31.58467 12.35967 6.437333 20.623 55.915 26.14833 14.54933 18.13133 32.75133 17.413 12.544 7.045667 260.6453 8.652333 10.51167 6.740333 36.07133 64.46467 3.101333 47.833 72.38467 19.68333 6.318 16.69133 16.16267 10.94967 22.98467 4.583667 15.947 16.40267 138.602 13.374 15.559 7.72 15.62833 27.02667 65.26833 15.246 28.212 84.71567 8.792667 73.07533 19.81633 118.617 14.42733 20.73367 26.33733 69.556 28.223 12.19033 7.913667 14.08133 5.709667 12.023 21.776 16.38067 18.174 499.6263 6.353667 7.566333 228.7547 14.411 19.28233 14.33167 14.10833 20.15033 18.108 14.04867 19.63133 15.44967 6.174667 9.647 18.931 67.14133 12.226 6.926 17.83733 7.395 10.679 9.231 3.122 58.535 14.50533 7.66 14.676 19.83467 37.02633 11.486 10.57833 8.412333 9.925 5.474333 10.23033 22.77967 13.91533 40.363 72.50367 2.032 2.410333 12.327 8.274 6.723333 21.41267 21.74733 23.04733 7.516667 6.977333 22.84267 7.087667 7.807333 0 2.177 4.98 4.895 9.294667 5.981333 15.98533 9.524 23.05433 17.25667 2.115333 8.525667 8.836 0.8883333 5.992 8.352 2.503 9.865667 5.685 10.462 1.723667 15.31167 15.28167 8.369 10.124 9.195667 5.838 17.55633 15.521 13.76033 4.789 3.596 21.67067 13.338 5.468 21.40333 11.013 6.127333 0.6243333 23.73867 13.31333 8.300333 10.828 5.664333 4.636667 0 11.173 2.327667 5.607667 9.423667 1.734333 10.288 0.1823333 5.763333 9.302667 23.191 0.4626667 29.664 13.186 4.385333 5.784File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset) passes test. 2953s 7.374 9.638667 9.153 3.51 8.232 1.195 0 18.65833 6.257667 0.093 3.68 3.465 5.190667 10.806 3.966667 6.641667 5.709333 5.354333 3.201 4.44 10.293 1.998667 4.074333 3.513333 3.158 2.341667 2.939 2.98 4.922 5.790333 0.668 5.685333 13.44 1.497 1.905667 2.409667 0 5.035 7.557333 2953s num discordant: 0 2953s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset 2953s sampleA_mean: 68.104 300.087 279.6767 558.1363 478.7223 641.1777 691.0767 620.406 98.85333 526.2243 96.61333 20.01233 103.6867 539.652 1406.461 850.6397 96.77733 260.666 251.019 876.482 954.153 536.193 1005.984 1005.984 655.8127 733.6827 360.2233 2.696667 45.76333 4.654333 72.55133 866.6187 35.44767 915.841 1220.149 113.178 81.319 5.762333 551.9577 967.4877 213.4847 950.0057 38.978 903.1557 861.8193 1117.319 15.838 20.97667 509.7623 555.952 1690.757 884.0843 93.42833 21.39933 17.37067 409.1913 98.448 2042.114 114.5207 1385.135 1784.069 16.51667 1545.514 1681.069 57.579 86.883 226.9223 443.633 504.111 33.62067 1094.775 15.04567 13.98533 866.9083 898.047 697.2287 121.0697 57.26933 128.1763 7.951667 425.357 1834.914 2466.545 1313.1 37.21967 1584.902 443.3597 642.0663 2590.581 224.904 56.797 223.9227 37.25567 11.583 603.456 9.434667 70.24967 393.3037 39.57833 33.57133 103.9153 62.50533 824.9103 759.571 7.212667 10.53633 18.754 76.41333 16.528 40.61467 4.244 3.078667 237.8803 1593.583 2.713333 118.9327 31.501 660.21 94.847 94.089 188.4693 39.67767 337.399 7.282667 1666.136 25.208 37.255 354.6413 22.92133 35.529 759.148 20.36667 141.697 75.48133 100.1173 71.78533 2166.993 2.398333 503.5693 27.52967 27.29 251.833 5.017333 29.18933 1796.241 28.45833 18.96267 23.04333 670.486 29.55 63.58333 325.5413 27.48633 6.167 560.8327 43.09833 14.91467 7.601333 18.88733 22.627 67.08167 5775.202 617.7277 42.57533 44.93767 47.34533 4.080333 1846.256 25.55733 15.73033 18.30633 6.546 17.221 64.19 35.29633 17.48067 27.59267 483.664 321.257 66.65833 497.7577 46.75733 65.027 51.407 10.30533 50.14667 40.23433 756.3963 77.21567 123.0927 6.496333 9.969333 6.745333 20.37167 16.54033 134.6073 15.08833 9.613667 74.00233 5.682 302.136 40.12067 37.942 42.16667 5.627 6.515667 31.92667 5.016 129.326 110.725 91.49933 2.280333 15.92433 27.23133 3.586667 47.651 30.828 2.177333 9.896333 43.50567 6.300667 14.33333 17.96533 22.74167 48.27367 3.595333 18.233 23.33733 16.27833 11.52 23.09367 34.16433 5.802333 7.963667 7.685 7.412333 28.839 18.592 4.745 15.54567 6.455667 1.292667 3.139 1.919333 275.3867 40.25467 5.474667 7.980667 20.135 12.30833 15.18033 66.73133 3.451 7.059 225.547 5.557333 7.909333 6.527333 73.59667 474.4033 14.71933 46.23067 1.460333 50.11167 9.824333 2.900667 48.562 2.592667 22.68433 8.791 73.27533 13.78833 61.43567 8.807333 8.292 27.61367 109.3627 25.71133 28.26467 18.317 15.46533 19.73 18.67133 49.835 22.375 11.312 33.815 30.97967 27.77367 7.083333 7.252667 12.40267 46.17067 9.274 2.154 6.248333 4.531333 0.838 4.766333 6.812333 6.929 44.97967 93.21667 59.43533 43.83633 5.733 25.73033 34.33067 112.283 10.12033 4.361 4.281667 49.788 29.26167 35.802 11.93267 17.59867 36.11867 25.40433 43.001 18.33267 13.64567 9.767333 7.869333 8.866333 23.127 46.73367 20.81133 24.63167 11.286 33.21467 1.991 8.002 13.58 15.25233 8.395 7.107 21.67167 5.895 2.068 266.444 3.200667 2.811 2.682667 25.089 0.8066667 7.48 8.631333 4.59 20.71867 17.53667 37.152 11.98267 6.686 87.024 14.93733 25.32233 15.94867 22.31833 3.516 3.293333 5.558333 9.773333 5.931333 2.433333 16.116 6.863 1001.993 1.851 21.32033 27.14367 12.79833 16.64833 30.75333 48.976 8.316667 16.899 9.616 7.782667 3.762 16.66533 7.766333 6.250667 21.06767 7.700667 15.01 31.12967 26.40167 7.226333 4.341667 5.364667 11.22367 17.85933 27.53867 0.713 27.83967 5.615667 8.077 6.204 13.22967 12.36433 12.753 74.79833 16.73 18.23433 15.57933 14.558 25.646 20.261 4.926 11.40267 22.93933 21.74467 14.18933 4064.721 2.723 2.534667 1.695333 7.884667 10.471 5.415 12.443 11.227 5.740333 2.800667 10.85033 5.603 5.421333 12.44167 16.40367 16.303 1.688667 1.288 24.758 9.105333 14.83533 2.243333 1.574667 3.424 12.394 13.71433 6.524 8.028 7.310333 95.166 12.388 12.76533 1956.885 275.0887 20.74967 1.160333 6.091333 5.630333 8.791667 7.585333 11.59067 7.711667 11.22367 13.106 12.90733 1.577 7.039 6.559667 22.17067 9.378667 9.510333 7.844 13.917 2.194 3.109667 12.14267 26.291 20.36133 6.380333 13.65367 9.436667 2.411 7.672667 34.157 6.778333 13.50467 9.471667 6.625333 7.621667 8.497 6.067667 8.578333 3.294667 63.63933 0.9146667 4.676 6.567 11.91033 10.12333 8.805333 2.818 3.857 3.09 17.75767 6.066 16.556 0.1093333 2.14 6.829333 8.293333 9.299667 10.72933 6.861667 1.363333 5.416333 3.468 19.73733 5.332667 9.694667 7.431333 11.94067 7.325667 11.36067 39.729 11.994 4.053 2.163667 17.19233 11.758 3.493 3.822 9.557333 4.963667 12.01933 3.301333 2.976667 0 3.165 0 0.01 23.38367 16.47133 2.758667 1.911333 6.521 3.736333 5.177333 4.482333 6.512667 26.67367 5.422333 0 15.47733 8.411333 10.216 10.201 1.302333 11.24533 5.581333 15.75333 0 6.813333 3.489667 1.897333 3.27 17.23067 1.407667 9.507333 3.680333 4.765 2.550333 7.337333 11.46067 0.248 8.343667 8.839 6.395 0 8.445667 6.326 4.196667 4.638 5.633333 4.293333 4.009 3.051 2.745 7.881333 0.6643333 4.127333 1.252 1.547 4.223333 2.578333 2.219333 0.409 6.606667 0.7683333 5.001333 0.4346667 2.605 4.484 3.268333 7.634333 2.517333 2.330333 1.184333 1.56 9.374333 1.870667 3.162667 21.42967 4.126 2.467333 1.384 3.090333 5.019333 9.984333 4.196 1.153667 2.692333 8.218333 3.043 1.351667 1.169 0 12.573 5.509667 1.637333 8.504333 3.979 3.021333 7.756333 35.02267 0.3906667 1.469333 1.980333 8.773 1.122 4.744333 10.61867 2.577667 3.393667 8.025 3.570667 2.448333 2.844 2.242667 4.724667 3.077333 3.682667 8.963667 0 19.30967 35.57467 1.344 8.003 4.41 2.335333 2.011 11.52467 4.52 0 3.484667 3.398 0 3.328 2.678 0.724 0.9123333 2.573667 2.944667 4.695333 2953s sampleB_mean: 1492.051 2827.345 7779.492 7520.41 5346.478 7181.47 9939.373 11165.49 2550.414 6944.853 1331.648 1076.978 1438.471 6464.644 10849.9 6705.697 971.4367 4978.607 2449.757 6887.084 7405.14 3982.392 8614.152 8614.152 4540.328 5036.385 4624.974 324.8553 440.9727 193.995 1007.03 5515.698 722.7793 6156.043 8313.711 1781.496 973.0083 155.6753 3325.992 5874.642 1506.715 8726.054 347.4017 5974.238 4809.412 7596.105 501.0717 303.273 3398.294 3104.744 11956.17 5589.41 1192.947 341.9023 217.5877 2649.173 819.1427 12136.75 876.8277 10695.83 8625.824 721.2523 9160.812 10005.84 512.042 880.4753 2510.784 2806.072 3101.543 318.3057 7921.826 147.2877 340.8923 5311.835 7137.863 5150.462 1183.775 644.756 850.5097 322.6313 3135.76 11807.78 12803.12 8077.68 337.5617 9231.562 2899.79 4181.758 14596.83 1237.565 498.566 1388.008 636.1717 188.059 3043.903 227.1767 493.2167 2813.865 381.4813 286.7303 803.7297 820.1 5402.498 5955.872 98.27667 224.959 176.1237 395.6523 210.5073 510.9113 88.77667 363.4697 1147.187 7646.521 135.6287 954.507 297.5633 3606.195 501.203 592.331 1232.959 437.8937 1727.754 304.1167 7998.991 434.5497 568.9407 2636.168 177.0987 277.6277 4659.391 237.9167 624.4283 369.4417 464.656 437.7077 12057.81 136.0917 2069.238 374.99 347.1993 1538.062 183.432 568.3683 7391.381 464.25 165.5147 227.959 3497.592 178.331 366.6233 1485.8 318.668 59.968 4052.112 365.9053 307.597 204.598 234.8707 257.8713 497.3057 31019.62 3477.406 221.5063 330.2803 309.0137 204.688 10466.26 229.8227 126.265 728.6047 124.821 209.5997 303.588 265.4807 361.7567 248.7967 2983.166 1573.052 365.304 2478.864 306.1523 744.834 346.0203 254.0923 223.6213 259.974 3680.324 617.5097 566.3103 96.888 76.629 115.6383 169.5693 159.9217 794.7277 102.4913 141.1233 434.0653 190.3363 1314.765 244.213 198.0453 228.616 148.3807 240.9067 205.964 133.1137 784.5 473.468 383.3883 91.93733 171.415 396.4167 107.6607 219.043 221.3943 132.997 130.7987 242.2357 58.786 198.031 153.6373 151.089 297.5293 92.04867 134.7863 146.225 201.1477 139.8577 332.1927 383.105 87.30767 189.81 53.11833 327.728 204.0893 160.6447 177.6103 196.2657 163.2497 65.022 293.4293 79.23 1190.783 243.0527 129.359 79.78767 171.2443 186.3673 106.9733 288.2643 85.369 118.4783 1374.415 41.92667 132.86 138.7943 324.095 1924.887 93.961 199.25 66.28233 208.997 165.6487 56.084 404.8233 199.5333 145.871 92.801 376.801 112.8707 261.1813 44.52667 71.07333 146.7367 502.0593 217.828 130.4647 92.66933 88.84733 108.0163 84.19433 317.4007 162.353 166.719 264.5573 155.6507 219.1713 51.48067 55.56067 110.12 241.8647 109.0163 38.50333 65.14433 102.4957 381.073 82.77467 175.727 65.82467 506.512 434.0367 451.6893 279.8187 79.15267 109.1297 189.876 446.5917 104.7473 565.0517 160.461 217.945 120.016 221.9553 92.14267 102.8277 210.276 150.83 251.6407 125.6427 142.4997 63.51467 49.84633 101.2043 125.9207 244.312 138.8203 102.9103 139.4217 147.5143 88.20067 72.04033 205.7273 138.9953 91.96267 72.27033 91.36867 72.229 54.28 1437.071 67.97633 42.94067 64.48933 313.5353 94.084 53.67933 98.42267 57.92467 94.855 88.724 329.0943 54.17467 92.354 391.7213 114.7247 147.9097 117.3687 188.654 615.4837 57.289 78.15767 94.036 98.59367 176.1103 359.4497 48.662 6554.638 59.07767 177.7223 111.3283 71.95633 112.4907 205.2823 272.869 62.202 80.658 92.10033 67.32633 136.3853 92.673 92.91767 578.1793 114.413 55.31033 75.13167 160.033 143.6177 63.519 58.84033 33.64933 54.697 89.19033 123.7103 60.909 126.6667 71.83833 52.40167 68.93667 92.58367 61.75633 98.25867 654.0063 70.82967 185.3687 83.32767 84.09433 189.338 97.67333 86.666 86.82867 143.2053 97.74133 106.367 23095.85 64.96333 31.92033 26.105 69.31567 51.40267 36.84367 55.42833 100.9357 49.55567 66.58633 60.39433 284.8557 40.88467 59.70833 91.34767 558.288 27.42533 23.09333 108.9977 44.59133 63.39167 25.16133 374.3023 36.129 63.275 80.30267 29.19933 37.13833 61.927 629.935 82.208 65.265 12433.72 1768.526 97.91867 29.412 30.305 28.11233 67.40867 57.38933 56.87433 37.373 47.69867 70.48667 74.47967 21.31667 59.309 65.641 101.2333 51.208 40.01867 44.65167 75.314 38.35733 52.62167 118.5717 105.9517 89.473 57.89033 58.72433 50.94033 20.836 36.83567 180.145 38.239 70.23367 53.35367 36.76167 39.14833 37.861 48.09067 51.20733 17.67167 269.8203 61.049 45.43467 40.58467 59.017 52.59533 40.58733 81.03933 46.01667 32.39167 72.092 44.57067 104.9537 58.52433 33.96833 63.80367 95.03067 39.439 43.553 74.76 33.71767 31.81733 22.795 89.41967 24.105 44.80233 42.02167 49.809 49.184 60.34067 170.7703 77.42067 24.42933 323.135 71.77333 83.02567 22.759 19.01033 43.199 24.998 58.53467 28.618 23.031 41.25767 16.98933 9.080667 16.39933 275.1827 65.63533 37.18267 19.87967 31.64467 50.351 42.55233 50.66867 134.3513 170.258 28.99667 8.385 64.17467 56.735 49.53233 45.68133 63.43233 59.187 31.359 63.14133 17.20333 34.963 79.93733 17.666 21.26833 69.73067 17.978 38.56967 28.08767 46.573 17.60767 80.83067 147.841 18.746 33.274 43.21967 35.30367 101.7453 72.57967 25.818 18.67167 39.557 79.05433 21.37133 21.925 19.069 25.20967 31.30167 12.13567 31.40267 16.692 27.15533 52.68633 28.28967 16.69733 40.14133 33.96667 12.81233 38.21633 9.165333 16.98933 38.06967 134.6853 62.14133 26.59233 16.53733 47.25833 22.82667 50.767 125.1613 13.12667 133.2117 18.98967 82.00433 45.292 13.31667 42.533 48.78233 37.97 58.21167 21.58933 69.305 15.914 8.173667 55.27767 44.84 122.654 24.348 14.71567 37.642 343.3797 51.753 37.89133 139.358 17.79667 11.03933 12.07167 51.325 10.06533 23.01233 45.16833 20.69233 23.021 43.66433 15.776 37.33167 13.166 19.56367 24.04433 30.44067 22.33433 63.401 11.09467 92.552 200.7123 10.878 34.98133 49.08533 18.31433 70.339 76.51933 29.65133 35.64 37.25433 14.291 29.38867 20.035 23.558 23.8 17.76433 22.41933 16.55933 130.2143 2953s num discordant: 0 2953s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset 2953s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test. 2953s sampleA_mean: 4954.434 1326.5 12222.46 2602.336 1751.765 887.2083 1445.705 1046.9 470.179 5495.505 2002.536 3549.085 637.4673 4784.861 5797.692 15024.4 36600.33 1833.283 1407.266 1371.045 521.84 1262.588 982.539 2635.243 1681.385 6030.232 944.0123 1816.62 335.7477 2191.464 1265.232 20787.35 4191.816 1013.064 4913.275 3468.578 1512.754 499.8527 1593.001 1718.763 559.8297 4713.887 1272.664 1291.39 1348.496 562.1487 647.4437 1233.492 1933.215 1656.826 1939.628 620.238 371.296 1707.219 999.5363 335.2157 1532.142 326.0873 2891.881 5395.606 1088.069 1091.041 772.306 1640.267 1037.645 810.3883 387.8127 176.112 363.4713 1120.621 2237.79 116.9527 258.5643 252.8977 5645.434 2017.126 5637.134 335.637 933.0403 178.6107 1753.538 1031.742 198.9307 923.62 925.3123 1179.723 388.648 564.1773 296.1627 581.2863 1434.927 531.0443 244.753 405.4877 154.4447 502.9777 425.4187 494.789 435.0017 594.819 876.645 590.469 2446.14 825.5967 533.844 393.785 234.695 460.3903 838.8547 405.9907 665.289 770.6237 567.2883 521.2813 1198.79 335.4993 1756.628 581.914 617.5563 194.6923 104.2153 734.0483 337.406 872.2057 762.2617 298.6353 233.2683 482.3557 1547.728 1707.261 322.1607 610.589 210.486 508.1423 854.0897 1125.723 664.8137 300.2583 480.5827 1412.697 244.4597 604.7417 209.749 114.123 337.767 563.9263 159.0503 568.889 1030.087 344.3147 146.7767 272.6143 122.4237 356.3497 150.8137 1315.006 182.1447 199.325 133.8673 437.1223 168.438 3088.486 991.437 122.591 99.45067 1229.376 407.805 350.3023 323.746 316.5037 719.3537 97.82467 349.218 100.0037 310.3323 219.039 432.0453 1099.802 499.693 89.41233 85.82433 156.591 176.9843 2769.091 147.324 89.249 240.267 519.577 310.3963 1023.96 721.5107 378.0157 109.0817 210.2437 407.6713 389.129 1606.153 562.891 207.397 114.485 201.4867 132.971 125.2723 207.939 120.7347 189.715 128.0267 294.269 164.5937 300.3533 3561.451 466.314 241.211 198.061 368.628 127.1483 471.4763 156.8307 1505.046 603.3643 328.3217 94.07567 71.71033 2036.308 116.1613 160.8853 103.573 177.4467 63.90033 60.22767 324.5383 115.35 161.1783 172.982 354.7773 122.177 212.7377 164.083 183.172 291.7607 62.56033 95.84833 421.348 80.98433 78.31633 105.1747 971.5327 192.5983 1557.898 81.80933 2465.916 250.2393 132.1053 169.0567 94.133 206.046 425.4893 304.6523 173.3993 104.0613 407.7717 84.98533 52.74467 363.302 91.99833 168.189 129.574 280.7067 59.607 98.94267 136.4807 124.4867 278.785 93.672 154.7137 66.11467 181.09 98.85333 236.6537 751.6327 55.68233 87.15633 78.67633 781.6647 62.65367 76.27033 305.3177 105.6967 93.57967 87.49733 135.433 354.898 280.1693 60.025 171.9977 204.4367 86.272 38.966 90.65667 4534.064 74.26433 40.38733 56.42633 51.06833 113.344 73.156 233.2737 66.544 47.17133 46.29267 54.279 214.102 53.23867 77.01533 66.88467 97.46133 62.81 44.27933 35.384 86.26767 64.515 496.4993 260.459 144.1087 93.98167 114.1953 38.21567 84.101 69.30367 194.3693 47.40267 27.49133 33.614 158.4977 37.746 51.68567 95.708 58.726 6075.931 51.916 32.07433 65.08533 630.4887 47.12267 101.362 56.34967 44.67767 471.7457 26.77667 50.39 35.92467 31.01767 42.52667 69.90667 37.93767 30.31033 40.76933 32.60533 82.45067 187.0867 71.55767 71.85 171.2653 40.022 50.27133 42.259 49.19267 131.435 56.78633 58.77867 45.27567 34.524 70.90433 269.428 27.86967 142.1963 16.066 38.467 38.41333 51.49667 33.66067 34.55067 163.5027 52.054 32.87767 10.913 141.5087 7.951667 56.986 115.2073 51.36633 41.489 209.263 42.42 24.04867 56.72833 43.001 20.61433 52.49167 19.379 45.48233 26.72567 42.69267 69.761 48.80533 32.359 40.90567 26.74467 84.52867 27.07933 32.296 19.36133 31.80833 28.112 92.064 35.653 23.66867 59.42133 132.0313 38.71367 45.49933 13.46233 20.89067 36.44033 66.32833 26.93367 191.9503 30.83533 73.985 23.675 23.51567 19.87867 59.42267 27.10933 23.62733 27.92067 27.69867 86.196 22.18367 31.895 43.59833 27.188 67.70667 23.94367 68.59733 14.442 26.41767 26.73867 23.232 22.01133 19.07933 27.52167 44.083 20.94233 13.58767 36.69767 28.092 20.15333 13.02633 27.81033 16.59667 20.281 22.07333 25.49633 14.06933 16.92233 422.5397 45.54267 20.21567 11.48267 2953s sampleB_mean: 175.0553 46.38933 644.6073 28.83167 11.541 11.73133 39.02467 21.734 14.071 10.731 60.698 54.76233 9.523667 176.7203 190.2367 126.2827 312.258 18.24467 61.93367 20.785 15.272 5.897667 38.35033 149.0183 34.85667 71.58533 40.62 3.02 17.87533 67.15133 70.315 1576.856 162.736 20.73967 231.01 143.0547 120.2997 10.32667 84.69133 167.6013 38.834 184.242 122.321 15.897 62.01667 41.809 18.007 131.954 91.85267 70.838 191.4833 5.31 11.974 199.414 52.632 18.10167 216.263 34.29367 107.587 4.892333 85.388 78.63867 52.029 172.0003 154.1127 97.40133 32.09667 10.14033 18.10667 4.916 176.0093 6.833333 20.43633 13.45833 1058.536 263.582 585.796 31.756 82.944 17.35367 290.869 146.7283 5.075 94.25133 167.5307 120.642 51.789 44.774 21.86767 69.84367 147.5103 59.39767 4.303333 68.43533 6.593 2.201 62.69867 7.353333 18.98533 21.75133 96.643 19.323 327.4777 138.9923 99.03833 46.20633 6.119333 86.94433 157.5777 33.76633 5.982333 76.85 5.055333 34.63 112.516 2.999 288.293 81.38067 35.93933 11.08667 10.803 1.413333 44.574 151.9077 60.149 29.81633 22.66633 78.18267 296.326 274.274 17.25433 119.8197 33.16933 111.2203 10.01733 239.1367 138.5447 8.328333 81.65333 4.947333 33.99767 135.326 6.52 5.291 57.83967 71.425 29.81667 98.93967 236.2837 48.44967 9.162667 14.93967 7.044667 45.153 13.40767 252.1407 31.26267 11.36967 18.47767 64.78833 24.10267 8.807333 228.12 5.435 11.37767 252.5313 80.735 68.39567 40.80033 66.14267 131.7207 10.11133 81.69867 7.705667 36.04767 31.115 62.152 262.4237 5.957333 11.83333 16.697 25.95767 33.04933 692.4403 29.03533 5.086333 46.24133 68.06833 1.439333 247.8637 64.61967 60.40333 9.454333 3.039667 77.499 52.96867 129.8027 92.249 22.379 12.202 37.04267 21.17867 22.86333 42.20867 4.436 31.045 15.958 60.023 15.18533 55.72533 52.72333 114.7383 52.859 43.10367 77.462 28.43733 103.8797 3.080667 300.8857 32.20767 46.83533 4.922 14.63133 456.8783 26.55867 19.13967 1.620333 41.19767 12.78767 12.457 44.73367 24.55133 33.53433 27.607 81.672 3.384 22.53 29.20433 41.53733 49.06433 9.876 20.181 77.08667 16.686 11.56533 20.32033 161.046 46.35533 221.51 6.152333 192.615 50.52767 28.67333 24.19267 13.001 27.23467 38.81867 72.39567 41.26233 14.93967 79.67267 11.13 3.457 72.445 21.33367 37.84833 25.094 57.499 9.053333 15.63733 23.92933 21.97267 38.40433 16.52467 36.59667 3.929667 29.328 16.70467 53.45667 131.0337 8.892333 10.136 2.519 0.8923333 14.59467 17.05033 58.95767 19.338 15.72 16.72967 30.64367 10.47367 10.048 12.56167 26.382 41.21667 4.478333 6.782 15.84233 1.982 14.317 7.813 6.818 3.424 26.43 3.546 47.94933 15.178 10.08733 6.808667 9.956333 49.04333 9.581333 15.967 10.61567 19.69133 11.71167 2.343667 2.932 13.70767 3.776 96.05 65.05167 22.72933 11.88467 25.736 7.134 9.684333 12.49533 41.753 9.795333 3.111 5.698 24.952 7.286 11.101 23.3 3.721 603.3247 9.442 2.596 15.82633 144.8737 10.034 8.861667 9.696333 9.568 63.54133 6.056667 8.024 5.451 6.028 8.245667 4.551667 5.482333 5.053 5.855333 6.225333 12.136 44.787 6.153 15.87967 6.163 2.558333 9.387667 6.709 9.898 23.79767 5.819667 13.348 10.75867 6.474667 15.06367 60.65633 5.932 34.28533 0 2.289 0.77 3.487 1.628667 4.229333 30.05333 9.460667 6.930333 0 5.704667 0 3.947333 0.8253333 10.76167 1.601 9.86 5.672667 4.175333 2.356667 6.886 2.932333 12.28333 2.445 4.818333 4.023 6.758333 16.034 4.762667 1.994333 4.880333 0 18.601 0 6.506333 2.312667 5.966667 5.907333 24.11533 7.766333 4.525 8.966667 26.49267 8.657333 3.518 2.201333 3.392 5.916667 2.695333 0.388 47.94667 7.344667 3.183333 0 1.805 3.583333 3.923 0 3.766667 2.298667 6.937333 1.362 5.132 5.972667 10.182 3.599 16.083 4.885 7.661333 0 2.759333 2.819 0.3263333 4.613333 4.606 2.479333 8.528 0.597 0.3683333 2.795333 1.379333 4.356 0 2.091333 2.582 1.481667 3.673667 0.774 1.082 3.048 25.345 4.943333 1.016667 1.101667 2953s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset) passes test. 2953s num discordant: 0 2953s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset 2953s sampleA_mean: 21.39933 88.57 72.55133 7.685 6.167 15.838 15.04567 224.904 40.988 102.2703 31.261 96.61333 103.6867 36.11867 121.0697 509.7623 28.64033 68.104 141.0787 30.97967 55.26267 803.1917 539.652 337.399 98.448 26.51267 76.15267 16.51667 655.8127 37.21967 503.5693 478.7223 46.17067 354.6413 504.111 279.6767 578.8703 10.53633 20.01233 526.2243 409.1913 733.6827 558.1363 4.654333 697.2287 5.762333 7.282667 57.26933 915.841 1275.026 291.1757 35.44767 18.96267 443.633 763.5533 2.713333 16.54033 81.319 620.406 641.1777 903.1557 7.963667 300.087 5.415 4.080333 40.83233 31.92667 125.9483 25.208 88.20633 96.77733 7.252667 4.244 11.583 7.212667 31.97667 850.6397 25.78433 425.357 115.4593 45.412 106.1753 78.96333 11.22367 188.4693 9.434667 223.9227 759.571 24.615 14.71933 31.501 209.5917 48.562 2.398333 47.34533 25.605 89.987 113.9973 691.0767 28.26467 159.4173 11.52 56.797 40.25467 33.62067 670.486 20.97667 171.0287 43.09833 26.208 497.7577 40.27 33.57133 13.98533 22.51133 15.54567 81.34233 2.068 23.04333 22.74167 110.725 50.11167 43.50567 18.76 23.33733 87.317 5.017333 12.993 642.0663 321.257 3.451 47.036 16.528 20.36667 23.127 55.73 37.27233 9.896333 443.3597 51.407 65.027 34.135 86.883 18.754 241.785 12.94133 7.980667 5.627 3.420333 393.3037 37.152 23.94067 260.666 19.92833 6.745333 57.46833 75.469 91.49933 87.42633 5.474667 17.48067 16.899 1.292667 79.21967 29.55 6.546 11.438 4.281667 13.46667 50.469 2.550333 225.8327 15.09333 5.682 39.67767 3.586667 3.078667 52.084 26.715 3.200667 66.65833 2.696667 27.29 26.67967 103.9153 9.969333 16.27833 18.317 9.642 2.280333 25.55733 55.59767 8.043333 6.919333 8.791 74.79833 22.68433 5.016 6.515667 7.059 15.73033 64.82733 15.92433 15.01 3.595333 103.2833 5.733 24.63167 37.25567 21.51767 5.557333 30.828 10.95167 27.48633 62.50533 11.312 18.88733 1.577 5.630333 11.227 7.909333 49.835 16.556 17.19067 1.460333 22.31233 15.18033 2.154 1.919333 2.177333 30.80767 17.96533 24.758 8.807333 14.063 18.233 18.30367 47.42233 2.811 17.221 2.243333 6.819 26.75667 4.745 10.216 10.30533 6.559667 4.766333 29.18933 44.93767 27.59267 44.996 19.11967 2.219333 27.83967 50.97333 4.371 18.62433 2.433333 5.802333 6.812333 7.844 9.735667 28.057 13.08133 23.09367 22.752 11.29367 21.116 3.468 5.931333 12.39433 20.261 26.291 6.455667 22.17067 3.941333 22.93933 12.98 13.65367 13.78833 20.37167 12.753 4.531333 15.08833 4.156333 4.59 7.48 27.94767 16.40367 8.497 7.039 37.255 23.67567 0.713 6.496333 6.980333 20.992 8.162667 8.316667 3.139 11.22367 9.507333 7.107 20.135 4.341667 33.01633 6.527333 18.94267 11.286 3.043 5.615667 12.36433 6.674 20.74967 1.991 31.32 28.45833 6.300667 32.849 42.16967 9.557333 84.312 6.929 2.330333 8.631333 5.895 14.94733 7.412333 0.8066667 44.07433 16.303 22.627 19.73 2.900667 1.911333 27.23133 9.613667 2.534667 77.21567 5.364667 8.077 40.34367 7.163 5.177333 30.424 11.93267 0.4346667 6.524 15.64 19.921 33.50367 28.33667 0.838 11.89067 8.403667 22.996 20.16567 2.592667 9.824333 7.354 4.963667 7.310333 9.767333 1.288 1.688667 8.578333 14.22267 14.78033 13.22967 7.884667 18.30633 11.817 18.33267 25.32233 3.857 8.002 14.06433 39.729 2.723 0.6643333 5.558333 12.40267 12.14267 0.7683333 15.57933 8.393333 17.692 9.773333 10.38333 25.40433 8.173 17.85933 28.43467 27.77367 1.469333 6.380333 35.802 21.06767 13.58 4.676 1.715333 21.69333 8.805333 7.050333 11.758 9.744667 18.23433 17.332 3.424 30.75333 11.994 14.91467 33.10033 7.083333 5.720333 7.216333 6.066 10.12033 9.616 14.16 8.866333 53.09233 7.672667 1.160333 6.248333 7.555333 1.162333 11.59067 2.411 12.76533 5.581333 3.162667 7.394333 6.910667 8.791667 0.1093333 11.36067 5.740333 0.3666667 1.695333 6.863 7.431333 11.21733 3.09 16.06567 5.416333 2.682667 44.679 10.85033 21.88733 6.204 2.976667 5.332667 11.097 0.485 18.93367 6.592 13.23767 4.926 7.585333 1.444 3.541667 20.36133 0.248 5.264 1.363333 8.395 5.603 6.067667 3.762 2.844 1.252 25.089 6.752667 7.766333 9.471667 0.9146667 3.109667 2.605 9.752333 0 0 5.596333 13.50467 10.201 6.861667 8.198 6.983667 1.302333 5.421333 8.351333 161.101 1.448333 2.715 21.32033 6.521 3.294667 2.818 2.745 5.057 1.897333 2.163667 2.14 7.621667 4.058 6.567 13.88733 12.883 7.601333 11.40267 15.09267 0 1.122 2.922 0.01 8.293333 7.325667 4.009 12.67933 1.351667 7.168667 3.765 0 8.038333 3.292 6.625333 23.38367 3.418667 0 1.574667 4.064333 4.638 3.822 18.91833 2.310667 0.4176667 4.053 1.769667 8.223667 36.09 1.281667 3.090333 6.754333 1.851 1.981333 8.255667 7.195333 7.337333 0 4.196 3.425333 0 2.800667 16.116 2.194 6.813333 8.773 5.060667 2.517333 6.512667 4.325333 1.089 0.7146667 2.474333 3.273 1.407667 1.994667 3.696333 4.572333 0.2473333 3.122667 2.883333 6.893667 4.765 3.493 3.293333 1.492667 1.649667 3.179 3.219333 0 1.576667 0 0.7693333 4.387 1.547 1.992333 1.344 4.989667 3.403333 0 1.980333 12.75533 2.347333 0.5473333 3.398 3.570667 2.877333 0.622 0 2.275333 3.733667 11.126 4.611667 0.9123333 7.756333 1.637333 0.409 2.663333 0.676 8.504333 2.337333 0.939 3.988333 2.414667 2.692333 2.448333 2.777667 3.992 1.56 3.319667 4.52 3.021333 2.577667 3.077333 4.451333 4.385333 6.45 2.578333 5.633333 0.4253333 2953s sampleB_mean: 1524.761 2830.628 1611.849 339.544 266.1853 2001.57 370.6363 3005.897 1440.661 2786.993 809.747 1997.885 1889.849 2415.454 2237.994 4325.944 686.1263 856.342 1374.611 566.031 953.5553 4759.337 3396.666 2883.64 875.9707 574.6353 759.8243 736.2793 3693.07 394.7987 3179.415 3249.388 768.1787 4198.375 3216.203 2471.048 3756.434 285.4657 344.6643 3330.022 2374.126 3620.716 2922.537 105.6647 4895.859 90.55133 437.971 556.5843 4427.58 5398.857 2047.901 421.1887 211.0497 2376.446 3709.705 149.84 253.343 630.4883 3616.512 2990.729 4251.336 472.5113 1235.974 208.1393 348.3133 562.3953 300.4817 606.0663 366.0723 476.768 485.2353 118.7197 73.643 144.7763 79.82167 279.329 3423.331 378.7327 2436.015 760.6557 241.776 731.863 439.0257 142.302 1094.26 146.4013 1049.838 5152.482 166.0277 140.0233 240.971 1034.454 692.2687 112.4467 298.0877 255.2837 683.449 461.5343 3650.525 194.996 927.6743 192.3193 366.123 332.1813 189.6917 3849.83 140.997 878.6043 341.4467 265.6093 3067.808 310.312 193.8653 164.205 155.4747 267.5577 401.21 205.6727 189.5857 171.3853 511.8627 267.723 269.2717 132.628 167.053 365.2543 132.7817 194.1133 2890.802 1547.523 120.2137 203.65 120.8233 165.0047 199.6 274.3337 218.6657 135.609 1780.032 321.7517 699.6877 320.243 404.5893 105.6257 1082.98 116.6347 87.31133 130.9923 58.96367 1642.015 609.5917 166.8767 1395.183 79.65933 90.86167 290.862 428.623 357.7387 434.556 140.1517 263.798 133.069 67.006 496.8353 127.811 84.91167 160.1683 317.0973 143.3147 286.777 156.2033 1012.972 253.0167 141.5657 254.1857 87.15567 105.0843 224.5063 178.71 125.4973 287.485 42.12067 212.3977 178.5933 444.0447 58.79033 177.3257 98.13967 90.957 68.593 160.4317 303.08 303.0437 92.061 97.3 1621.57 150.3183 96.602 165.4787 109.1813 88.38 255.8583 133.1023 117.2697 71.08433 443.3713 96.957 127.943 260.6683 96.142 38.85333 175.8867 127.5543 189.0233 382.3843 177.183 138.4137 83.61967 55.55933 240.6073 118.3287 351.08 385.176 132.4173 60.04567 161.1673 90.116 39.998 59.379 81.26567 125.2547 115.1327 193.4727 40.32533 75.75133 107.4287 150.3003 252.983 57.69533 123.721 65.65667 85.78933 213.8997 120.4613 195.2947 140.2763 183.3313 79.68 259.148 207.045 149.819 231.7267 120.8867 151.719 168.0607 232.1147 51.73767 83.573 382.0493 58.06633 166.5273 92.43267 91.509 218.8733 91.18133 216.949 194.3873 59.23867 95.749 64.25433 131.585 53.59967 140.8457 199.317 103.81 184.3507 31.73 220.7547 74.99667 108.7427 88.725 101.0153 134.7907 82.67333 62.39367 87.65567 60.63 57.40167 162.3163 143.607 72.854 123.938 229.5497 143.433 136.4467 48.27933 67.408 87.012 69.18967 67.72533 126.504 74.632 109.6237 69.947 116.5553 76.57167 183.9787 85.55767 176.0977 132.2 117.851 93.48367 71.93733 59.629 145.5417 80.46333 148.7563 186.8647 33.62833 151.599 178.2697 96.76 473.3597 49.419 119.8297 90.91333 61.29533 138.9263 136.346 80.36 177.785 1604.347 110.8577 78.48367 32.967 72.596 195.6537 62.05533 43.412 323.664 34.301 53.67167 161.956 293.9087 133.338 124.6713 68.66267 177.154 35.42167 89.57667 118.1207 143.872 174.409 104.978 106.4977 71.28167 136.4563 102.0507 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test. 2953s 71.74267 84.66667 41.93 47.35667 80.51633 45.994 30.70733 36.13033 77.97333 71.81167 96.91167 84.28567 76.68167 188.329 53.655 88.05067 114.4257 83.324 48.91 69.52233 280.2713 69.599 84.001 56.562 63.03733 183.6017 96.94267 78.28033 51.723 127.9993 67.53533 71.949 100.6683 50.22033 77.092 188.4637 123.1273 68.608 79.551 142.4753 90.31267 126.4583 65.56833 36.53367 311.329 49.36433 36.76567 150.4293 68.67667 159.7823 68.32067 34.95467 151.883 120.206 77.38367 137.8557 27.671 39.086 36.70233 57.43267 55.85733 63.84367 76.47533 53.52367 356.891 40.14733 28.55333 30.21933 29.627 61.53933 53.014 22.85467 61.12667 48.22433 29.26867 47.69067 27.296 61.486 161.9667 76.577 38.799 36.6 19.45267 30.35033 51.13867 73.193 37.55767 84.252 37.65433 27.28933 191.3687 48.89833 106.615 43.65367 31.70567 27.176 47.47333 76.24933 100.608 48.224 62.81267 58.25633 43.97967 59.38567 33.21433 84.57567 82.68433 44.01933 41.03967 42.95633 186.3597 45.60867 57.43367 35.499 36.72267 149.342 65.255 52.33733 49.472 61.21367 44.45533 33.399 42.28633 22.75467 251.767 40.13033 62.27133 55.77667 79.067 32.39667 37.29667 130.8803 27.93333 58.12767 885.105 127.1577 33.473 91.86567 35.098 14.628 67.063 39.59267 34.77567 21.83433 423.253 22.669 31.972 27.94833 33.70267 69.843 50.84367 31.336 50.05667 61.76067 7.787333 27.11633 16.267 18.93767 79.87367 42.60033 26.188 61.23533 14.83167 31.52433 28.714 7.434333 38.139 33.73067 25.97433 329.1877 32.58033 19.23067 84.23433 30.03567 46.144 15.205 107.6573 31.73667 19.80633 17.84967 27.04033 117.513 166.674 20.92033 16.67967 37.849 13.23833 49.82833 49.72933 30.596 77.94767 20.285 56.93233 15.277 86.78467 22.274 95.334 16.95033 27.944 78.66133 26.27467 30.23233 98.03267 22.413 15.25033 73.018 33.19833 18.09167 12.861 18.55533 26.23633 37.429 19.36667 15.02733 28.15867 28.39433 34.77033 13.99333 13.36767 20.05633 18.50433 20.35933 29.242 30.69133 17.502 18.48833 17.31067 21.34167 19.614 30.54067 13.94367 65.14467 18.03233 3.268 12.443 66.67867 12.703 28.44433 16.01333 16.27233 15.656 17.43 31.383 17.236 70.27367 80.966 22.38467 24.30433 38.17233 13.41633 18.61167 15.33767 31.89 37.68333 23.945 23.73133 15.90267 38.715 17.96033 39.09833 19.04733 16.55367 15.269 14.817 29.889 46.892 17.898 28.101 32.61467 18.28267 62.73233 15.10167 41.99133 13.18233 2953s num discordant: 0 2953s validating: Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset 2953s File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test. 2953s sampleA_mean: 768.306 1781.496 876.8277 1636.976 4624.974 512.042 12470.43 440.9727 834.608 324.8553 871.6373 2550.414 1506.715 1101.219 707.8263 3078.184 347.4017 217.5877 177.0987 493.2167 31019.62 850.5097 514.415 501.203 224.469 510.9113 339.8283 620.017 1098.868 95.89333 2373.043 1192.947 621.286 645.4617 198.0453 856.7063 411.447 3211.031 646.6133 429.5973 173.88 189.5647 1003.238 244.213 222.09 474.0487 689.711 1494.298 306.1523 237.177 900.1817 374.99 328.0923 211.7417 623.5437 646.864 204.598 378.627 166.336 194.2893 132.9247 661.7387 257.3087 198.031 151.8027 97.24867 138.8203 109.0163 88.61667 116.0807 499.6263 103.6453 75.79967 189.876 153.4527 565.0517 194.0203 186.3673 615.4837 149.5763 202.739 188.654 92.354 63.519 506.512 215.8967 91.645 53.598 276.1017 175.2467 160.284 272.869 112.6127 278.7853 189.338 103.0963 37.50533 583.86 374.3023 161.0497 131.159 578.1793 114.7247 138.9953 72.98133 322.6313 45.62033 100.247 112.168 2633.716 54.95833 94.455 63.24267 39.40267 214.853 46.03533 55.41567 59.07767 57.289 82.208 51.208 58.90833 106.367 114.2777 80.30267 55.17567 359.4497 541.9867 66.74667 103.33 43.62667 31.404 99.289 29.69867 30.70067 52.59533 36.49633 46.59433 75.16967 227.2843 83.27833 170.258 69.91033 41.25767 39.44033 28.455 40.44433 39.745 28.618 50.351 32.245 137.7607 35.30367 13.208 63.80367 43.80133 25.087 33.46233 81.69967 72.57967 42.52533 50.66867 36.466 82.00433 40.18733 72.777 27.874 24.83067 134.6853 75.28167 38.06967 79.93733 19.68333 37.18267 124.9103 25.539 48.025 7.618667 23.51433 58.47233 24.891 31.40267 92.552 25.74867 50.767 57.61033 18.93167 56.21533 147.841 48.78233 62.14133 45.16833 22.33433 31.79067 29.71933 48.16367 23.021 29.06367 63.71067 20.62167 63.05533 26.44133 76.51933 22.32333 69.305 101.7453 31.89567 55.27767 68.14433 59.28433 122.654 28.191 36.90167 23.01233 27.69933 18.868 93.41733 19.09633 11.958 45.292 18.83133 49.08533 32.10933 27.838 31.779 52.69467 19.622 19.95933 67.73133 72.11233 26.81733 22.708 64.09967 19.45967 43.573 23.05967 37.914 57.80667 2953s sampleB_mean: 11.541 78.223 59.789 131.954 341.9077 41.31433 312.258 21.142 149.042 42.12067 107.8423 16.70467 165.372 143.015 84.293 644.6073 72.11933 33.19 18.75567 77.04167 8202.657 173.185 28.83167 107.4767 15.272 17.62467 40.62 19.323 162.736 6.833333 8.807333 230.7603 70.838 98.93967 17.10933 147.5103 51.37267 176.0093 84.69133 60.698 11.974 21.17867 231.01 24.36067 40.211 62.01667 91.85267 361.5717 60.63 52.02367 190.2367 63.14733 1.413333 47.04433 149.0183 126.507 31.336 50.806 8.328333 15.897 22.66633 126.2827 52.632 35.05467 21.67633 20.43633 21.66667 14.771 4.436 23.35133 52.72333 13.34567 14.72967 43.86567 22.414 3.203 27.23467 44.21233 3.97 30.432 35.93933 25.96333 11.42567 4.816667 113.391 43.19967 15.47833 7.705667 49.04333 36.80733 5.957333 61.038 3.546 38.81867 5.980333 15.84233 6.593 126.723 84.23433 34.63 21.75133 5.375333 27.299 33.24633 15.958 0 6.119333 21.97267 20.231 603.3247 11.08667 7.766333 6.474667 1.620333 47.94933 3.929667 11.73133 13.23833 13.36767 14.15433 7.976 7.353333 21.74967 24.79367 15.00967 5.855333 95.334 101.151 15.63733 21.066 4.916 7.205333 22.53 1.439333 6.552 10.64267 2.201333 6.709 15.06367 53.09067 8.861667 21.36367 4.875667 3.745333 4.478333 3.039667 7.920333 7.033333 3.831 2.48 6.818 34.28533 3.374 0 14.63867 5.966667 5.451 2.116667 19.603 1.932 0 0.6883333 6.506333 0 6.937333 14.62267 6.301667 1.628667 12.223 7.897667 3.003333 14.45 3.384 8.477667 21.018 4.024 4.954667 0 5.055333 8.693333 2.909667 6.082333 8.839667 3.431333 10.157 6.500333 1.101667 12.1 41.35533 10.15367 9.771667 9.145 1.765 7.386333 2.893333 7.749 2.511 1.569 10.28 1.082 5.157 4.422333 8.006333 1.63 13.05267 25.41533 6.758333 3.485333 1.799 5.139 19.24567 2.819 8.017333 4.993333 0.692 2.849667 14.763 0.4836667 2.343667 10.16333 4.229333 5.657333 2.181667 0.8023333 1.487333 5.417 2.936333 3.54 5.873 16.907 5.261333 4.677 9.295333 4.786667 2.462333 4.158333 8.735 2.217667 2953s num discordant: 0 2953s validating: Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset 2953s sampleA_mean: 825.1763 1020.23 311.829 2661.226 28.62567 53.11833 37.23367 658.8357 110.7323 773.7893 117.2063 534.2237 112.322 77.55333 407.2907 94.08633 210.276 135.901 191.8153 501.0717 95.99433 62.58133 220.5287 138.353 59.968 341.9023 40.96933 105.9497 88.495 189.9813 4.98 81.05967 53.687 73.97767 16.50567 36.99433 65.965 24.33867 115.6623 50.429 124.4243 55.75367 56.147 17.029 30.499 104.7537 62.68467 83.305 25.096 63.41767 21.54267 132.8633 42.797 48.72833 36.84367 56.695 336.3973 49.103 180.8457 12.544 12.42267 9.165333 14.554 40.53433 53.33433 57.313 15.418 58.24233 68.49367 47.89667 39.58367 103.5143 17.60767 9.605 19.86033 3.969667 32.75133 2.172 17.875 6.042667 25.39133 30.00467 24.273 39.777 41.856 199.8083 21.25867 31.04633 35.78433 11.277 8.516333 342.208 22.84267 45.89833 20.959 42.71533 16.69733 10.63267 21.14433 31.838 57.13467 41.83033 7.538 23.53367 24.02367 15.26033 16.22733 70.13033 91.47333 35.43333 24.772 29.33233 5.832 3.122 28.28467 7.374 5.607667 36.41067 24.38833 133.0233 31.61067 14.56933 14.411 12.023 23.71433 40.92067 12.36 15.559 7.083 13.52433 7.960667 29.44033 75.059 88.60033 15.28167 5.097667 56.92767 12.85033 43.318 8.362 6.926 3.966667 21.31667 6.314 21.88967 25.25367 8.268 10.23233 16.53733 24.662 16.38067 17.12667 12.771 15.914 40.359 20.27767 12.81233 6.981333 12.13567 22.77967 21.02533 10.30967 7.979667 10.16833 23.029 2.752667 8.47 65.86733 10.49233 5.664333 7.825667 2.792667 5.342333 18.746 3.51 21.765 49.53233 6.437333 11.38633 5.772333 238.9387 27.34567 5.960667 28.07033 20.79733 7.526667 2.727 19.21233 9.187667 3.596 8.79 11.90333 4.820333 15.31167 21.686 18.06167 16.75833 54.65067 46.84667 5.464 37.02633 17.25667 2.539333 3.046667 5.197667 21.776 14.33467 22.029 22.86533 0 11.28667 8.792667 23.46733 14.50533 7.951 5.777667 11.03933 6.225667 12.438 3.531333 32.918 16.17933 6.306667 8.809 7.603667 29.746 74.98367 10.73033 8.48 7.113667 7.839333 6.174667 78.08667 5.639333 22.12067 14.356 5.177333 5.134333 7.025 6.934 0.8883333 3.201 3.158 8.591 13.76033 12.918 7.395 3.788 10.31933 1.752333 1.506333 9.925 3.503 8.232 9.197667 7.014667 7.501667 0 5.081 4.237 2.409667 0 3.773667 3.867 7.901333 5.981333 2.654667 6.052333 2.742667 4.912333 0 2.518667 0 2.723333 3.633333 2.993667 6.318 7.077333 1.934333 0.093 9.321667 2.414667 23.97033 19.63133 5.407667 9.876 7.560667 2.888 6.688 4.064667 2.503 2.105667 2.653333 7.296333 0.2506667 3.311333 10.97667 4.158 2.967333 2.349 3.471667 1.734 4.931333 0.5686667 8.351 6.958667 2.231667 0 5.76 0 10.806 2.677333 3.945333 0.4486667 6.261 5.397667 7.922333 2.362667 4.514333 1.742333 2.98 3.743 2953s sampleB_mean: 3756.434 5398.857 2830.628 13329.63 317.4807 339.544 461.5343 4216.251 1202.982 3709.705 3506.467 4004.8 2786.993 809.747 2355.907 968.2863 2415.454 807.5603 1242.884 2001.57 878.6043 843.2847 2047.901 953.5553 266.1853 1524.761 501.3557 686.1263 574.6353 926.6357 1440.661 786.1327 256.6427 805.275 584.575 279.329 317.8843 203.078 720.0863 573.2667 513.784 222.0223 562.3953 286.777 378.7327 468.317 303.08 401.8723 166.0277 477.213 255.2837 641.6557 255.0223 224.5063 208.1393 387.0143 1576.856 290.862 1012.972 137.7833 166.8767 177.154 148.789 682.0817 371.2327 255.8583 194.1133 310.312 585.796 265.6093 320.243 496.8353 156.2033 109.3147 121.5623 59.23867 219.6953 58.96367 116.6347 90.957 156.0383 125.2547 145.604 157.5777 278.7393 1109.48 168.2893 163.1987 178.71 110.8993 127.5543 1834.421 301.9357 178.2697 143.3147 263.0527 151.719 92.061 213.8997 263.5397 232.1147 195.216 303.0437 132.4173 150.3003 124.6713 194.3873 311.44 405.776 160.5167 163.021 161.1673 91.509 91.739 145.137 143.872 99.863 148.6807 148.7563 1082.98 160.1683 91.18133 179.874 96.804 120.8867 161.4237 101.4477 108.837 64.25433 57.44367 98.33933 151.599 332.2983 437.7257 143.0897 87.65567 253.0167 70.221 193.3587 51.73767 41.78967 102.0507 83.61967 71.81167 109.0193 174.6973 67.408 69.18967 119.8297 176.0977 109.6677 85.78933 118.1207 117.851 188.56 138.9263 96.94267 31.73 84.001 918.9367 293.9087 53.655 192.615 46.842 113.004 29.627 96.91167 285.3807 48.96533 47.31267 60.90233 76.24933 24.80467 82.68433 37.96133 141.0183 195.2947 56.05633 64.15933 51.723 4759.337 174.409 50.22033 126.6913 125.7047 71.949 36.6 107.2877 54.097 27.192 41.93 63.62167 68.67667 130.4127 141.442 91.49033 76.82 230.7707 216.4093 36.76567 191.0543 317.6723 32.39667 29.675 27.296 90.427 106.615 127.9993 97.60633 174.965 84.252 44.98367 169.1617 216.4057 44.69833 251.767 68.608 61.53933 311.329 36.53367 170.7463 93.09033 41.517 49.09733 127.1577 120.0493 381.953 55.476 39.086 61.76067 34.05967 28.425 356.891 59.38567 112.8043 73.193 30.54067 40.13033 58.12767 43.94933 19.95267 31.46 30.93667 65.255 76.899 52.36933 28.775 24.244 48.14767 33.473 18.20933 41.50267 20.82433 42.92033 61.80233 27.23833 31.52433 24.882 54.54667 15.87267 16.15667 19.80633 24.241 30.03567 34.77567 24.384 28.39433 27.607 22.782 33.73067 18.23433 26.27467 6.507333 31.73667 19.99067 15.938 129.8027 28.714 28.30833 12.004 44.13267 20.92033 106.4977 178.6527 21.00233 49.72933 32.58033 23.60467 68.356 27.04033 11.60833 28.15867 33.19833 33.75167 19.36667 18.612 73.018 20.046 12.202 86.78467 14.948 19.23067 20.212 18.004 54.89133 80.966 17.502 3.268 28.421 31.383 68.52333 72.35433 20.05633 16.761 25.473 21.03667 70.27367 17.43 23.30167 38.715 16.92567 15.33767 2953s num discordant: 0 2953s File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test. 2953s touch test_DESeq2 2953s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method voom -s samples.txt -o voom_outdir 2953s $VAR1 = { 2953s 'wt_GSNO' => [ 2953s 'wt_GSNO_1', 2953s 'wt_GSNO_2', 2953s 'wt_GSNO_3' 2953s ], 2953s 'wt_ph8' => [ 2953s 'wt_ph8_1', 2953s 'wt_ph8_2', 2953s 'wt_ph8_3' 2953s ], 2953s 'wt_37' => [ 2953s 'wt_37_1', 2953s 'wt_37_2', 2953s 'wt_37_3' 2953s ] 2953s }; 2953s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.wt_37.vs.wt_GSNO.voom.Rscript 2953s Got 9 samples, and got: 10 data fields. 2953s Header: wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 2953s Next: TR24|c0_g1_i1 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00 2953s 2953s $VAR1 = { 2953s 'wt_GSNO_2' => 6, 2953s 'wt_GSNO_3' => 4, 2953s 'wt_37_3' => 2, 2953s 'wt_ph8_2' => 9, 2953s 'wt_ph8_1' => 8, 2953s 'wt_37_1' => 3, 2953s 'wt_37_2' => 1, 2953s 'wt_GSNO_1' => 5, 2953s 'wt_ph8_3' => 7 2953s }; 2953s Contrasts to perform are: $VAR1 = [ 2953s [ 2953s 'wt_37', 2953s 'wt_GSNO' 2953s ], 2953s [ 2953s 'wt_37', 2953s 'wt_ph8' 2953s ], 2953s [ 2953s 'wt_GSNO', 2953s 'wt_ph8' 2953s ] 2953s ]; 2953s Loading required package: limma 2955s null device 2955s 1 2955s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.wt_37.vs.wt_ph8.voom.Rscript 2955s Loading required package: limma 2957s null device 2957s 1 2957s CMD: Rscript Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.wt_GSNO.vs.wt_ph8.voom.Rscript 2957s Loading required package: limma 2959s null device 2959s 1 2959s cd voom_outdir && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl \ 2959s --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt && \ 2959s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt 2959s 2959s 2959s ** Found 1817 features as differentially expressed. 2959s 2959s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR -m diffExpr.P0.001_C2.matrix --log2 --heatmap --min_colSums 0 --min_rowSums 0 --gene_dist euclidean --sample_dist euclidean --sample_cor_matrix --center_rows --save -s ../samples.txt 2960s CMD: Rscript diffExpr.P0.001_C2.matrix.R 2960s Loading required package: BiocGenerics 2960s 2960s Attaching package: ‘BiocGenerics’ 2960s 2960s The following objects are masked from ‘package:stats’: 2960s 2960s IQR, mad, sd, var, xtabs 2960s 2960s The following objects are masked from ‘package:base’: 2960s 2960s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 2960s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 2960s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 2960s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 2960s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 2960s tapply, union, unique, unsplit, which.max, which.min 2960s 2960s Welcome to Bioconductor 2960s 2960s Vignettes contain introductory material; view with 2960s 'browseVignettes()'. To cite Bioconductor, see 2960s 'citation("Biobase")', and for packages 'citation("pkgname")'. 2960s 2961s 2961s Attaching package: ‘fastcluster’ 2961s 2961s The following object is masked from ‘package:stats’: 2961s 2961s hclust 2961s 2961s [1] "Reading matrix file." 2962s for plotting:: min.raw: -0.680559894057534 max.raw: 1 2962s null device 2962s 1 2963s for plotting:: min.raw: -7.50284849776958 max.raw: 7.50284849776958 2963s null device 2963s 1 2964s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_37-UP.subset 2964s sampleA_mean: 6030.232 20787.35 1833.283 1407.266 1046.9 4776.171 2191.464 4954.434 1371.045 1037.645 1013.064 1326.5 982.539 484.398File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_37-UP.subset) passes test. 2964s 887.2083 559.8297 2059.192 522.8673 335.7477 1681.385 1262.588 838.8547 533.844 499.8527 4182.673 1066.12 11423.35 5797.692 545.5957 1532.142 562.1487 333.5833 470.179 1120.621 810.3883 1445.705 1707.219 1512.754 2616.495 301.1237 409.7437 2460.887 2442.782 2602.336 3549.085 480.5827 604.7417 581.2863 4784.861 629 502.9777 941.4197 1319.258 4913.275 15024.4 1272.664 400.0377 323.5933 647.4437 620.238 1265.232 508.1423 134.168 1816.62 338.9207 1718.763 198.8237 530.7697 1088.069 2635.243 923.62 1753.538 425.4187 350.1547 180.1727 335.637 296.1627 178.6107 637.4673 298.6353 388.648 203.246 872.2057 564.1773 1326.869 249.8873 1939.628 933.0403 393.785 373.2207 207.4947 731.256 335.2157 579.459 104.2153 914.4587 218.991 3468.578 772.306 1291.39 456.1583 693.0703 5637.134 1640.267 665.289 494.789 599.1197 744.858 481.5627 2207.998 339.0793 252.8977 350.3023 584.709 876.645 579.619 583.6803 4713.887 419.6373 182.1447 134.0677 323.2733 2002.536 1315.006 1229.376 124.028 150.8137 119.932 167.1063 435.0017 127.1483 719.3537 567.2883 201.4867 2446.14 482.3557 177.4467 490.2657 85.82433 340.5557 148.374 742.0153 221.959 991.437 154.4447 272.6143 209.749 310.3963 2891.881 505.6607 161.9753 198.9307 455.3783 510.4197 211.844 363.4713 1214.03 762.2617 197.342 711.3287 1099.802 354.781 446.9747 313.843 1547.728 210.486 156.591 241.211 256.9907 262.1497 574.8767 219.039 123.246 912.636 1125.723 122.234 244.753 407.805 352.3153 243.9703 189.715 387.8127 676.234 300.3533 854.0897 2688.784 323.746 318.1197 243.326 183.172 99.45067 231.4073 176.9843 62.56033 690.4453 196.6567 168.189 334.935 146.7767 71.71033 303.8613 432.0453 97.82467 234.695 252.697 162.433 369.791 192.5983 330.6623 122.4237 1815.027 1412.697 152.1197 356.3497 783.8573 563.9263 5395.606 216.15 83.207 594.819 83.07667 356.783 250.2393 67.469 617.054 57.64267 114.123 60.22767 114.485 294.269 78.31633 97.23167 407.6713 136.2463 342.712 110.791 160.8853 109.0817 160.1673 86.386 310.3323 122.177 210.2437 324.5383 122.591 76.27033 87.49733 322.742 112.757 240.267 328.3217 322.1607 118.5347 320.023 239.7997 111.007 69.89367 421.348 299.966 334.361 371.817 93.672 94.07567 571.859 133.1057 199.325 104.0613 75.336 207.397 132.6493 62.65367 335.4993 33.26767 144.7257 172.982 115.132 81.80933 99.03533 91.61633 86.67367 280.7067 31.38733 76.09067 228.911 169.0567 134.6873 306.508 42.552 1557.898 64.34933 79.282 32.351 6660.051 85.95367 55.68233 110.5993 721.5107 78.67633 89.249 59.60267 108.859 38.966 52.74467 105.6967 135.433 307.9013 363.302 80.98433 112.5293 58.232 781.6647 94.69467 93.57967 220.177 67.206 114.563 94.133 79.07433 84.972 361.8817 204.481 46.65767 31.766 62.81 84.25 155.7297 77.01533 38.21567 3561.451 98.302 89.883 156.8307 91.79433 84.98533 73.806 603.3643 44.71033 47.17133 172.4453 30.17067 112.7063 66.88467 41.339 38.01367 56.34967 87.15633 67.623 398.1303 526.9727 35.384 39.99867 32.60533 74.26433 158.1847 47.40267 73.085 64.40333 69.72667 112.884 2952.358 100.0123 37.59833 176.214 47.775 51.06833 69.21367 144.1087 32.07433 34.95267 74.20533 71.85 2465.916 32 5495.505 23.42167 103.086 44.67767 131.435 20.93567 26.93367 53.25667 49.19267 69.90667 39.204 164.921 78.667 56.22233 31.13533 16.46033 52.91967 279.711 43.95233 1172.149 66.12467 21.82767 30.96067 54.81767 171.2653 31.01767 40.988 306.441 64.515 340.941 38.41333 703.739 31.93633 168.4167 65.34533 27.49133 33.50367 38.414 50.27133 280.1693 354.898 40.022 34.237 14.64167 95.708 115.173 37.93767 163.5027 405.356 197.0237 84.101 52.49167 442.0453 37.304 38.44933 85.27667 51.916 52.662 69.92267 71.55767 15.47467 29.75167 1606.153 15.402 56.78633 42.42 36.76933 20.16567 89.08767 24.04867 35.23567 551.5827 58.726 4534.064 84.52867 106.8033 115.2073 28.112 16.59667 41.489 36.44033 23.34767 14.82667 9.429667 20.02467 16.066 14.972 23.62733 19.56433 16.558 23.565 8.473333 246.2103 35.217 36.86033 88.74833 24.90267 66.32833 10.73367 33.16667 26.74467 27.81033 209.263 158.4163 23.36033 15.77833 22.18367 176.112 38.71367 40.90567 9.629333 20.61433 2964s sampleB_mean: 173.6673 336.3973 63.97333 33.63533 27.41467 543.417 98.61433 175.7007 28.87167 47.461 18.23967 98.97567 33.35533 24.33867 55.41567 32.483 313.6673 28.62567 21.376 10.849 9.133333 39.777 47.52733 18.18567 658.8357 183.983 534.2237 900.1817 72.053 225.2773 52.09567 36.39433 10.76867 43.62667 63.963 139.4193 218.998 281.149 629.0693 55.75367 42.68733 73.97767 563.4113 514.415 84.42267 39.797 95.47967 27.60133 299.0663 94.08633 9.088 232.083 117.2063 1003.238 661.7387 217.05 24.273 38.47567 49.48767 12.49967 250.9827 79.409 13.52433 3.202333 50.10333 296.743 22.41533 110.7323 145.798 623.5437 79.21633 375.202 72.874 36.41067 27.94467 74.29867 8.580333 32.70533 2.778333 26.58267 85.85133 32.93 116.6427 68.27467 191.8153 36.231 297.3653 143.4493 68.88567 53.687 28.87667 170.8453 43.422 102.7107 14.398 213.755 48.99067 457.8803 68.979 194.2893 80.21667 150.937 68.49367 280.8763 12.67333 58.90833 130.483 132.8633 105.7627 412.998 70.59233 15.51133 19.23033 122.476 94.216 113.0753 85.73633 338.805 50.429 18.134 23.18133 25.39133 429.5973 131.764 124.0153 15.837 10.44 22.87333 33.283 66.97833 14.087 119.1803 23.51433 23.402 582.8023 70.27367 21.00533 44.471 10.49667 72.46567 9.605 62.58133 45.02367 223.4383 37.50533 38.81867 15.964 29.69867 125.8543 118.5987 35.82667 5.223667 92.838 126.7297 29.54433 12.30667 230.2087 43.57767 29.96067 118.5947 170.561 80.928 88.46167 74.91 377.1183 32.109 30.82233 22.455 62.40367 40.96933 56.695 9.034667 29.317 115.6623 261.706 10.49233 5.388667 58.22233 56.458 60.89033 31.15267 89.28567 116.0857 29.063 11.05733 462.724 38.353 73.76233 43.417 26.18 10.675 7.825667 39.035 11.399 154.972 42.91667 28.625 64.78933 32.132 10.603 49.50333 70.388 10.31967 45.62033 52.69567 11.277 70.13033 26.01033 43.27 3.616 402.3693 4.412333 26.68733 58.833 170.3357 120.0037 4.127667 45.433 20.623 131.159 18.13133 68.36967 48.89067 8.652333 115.9157 13.374 2.461333 12.03667 2.967333 55.04367 14.54933 22.98467 96.276 14.554 71.40267 26.685 14.26033 19.12733 36.07133 15.947 21.807 19.68333 28.455 55.915 8.546333 15.62833 6.740333 73.756 12.85033 44.52567 43.231 6.660667 28.90033 71.137 41.856 11.71333 8.867667 75.955 72.38467 72.094 78.80367 16.16267 12.35967 87.39733 24.22767 20.14333 16.69133 6.437333 47.833 33.48033 4.263 2.287 6.353667 29.59733 6.052333 26.14833 10.94967 19.23 15.559 17.759 65.26833 6.926 14.33167 40.359 14.82467 31.58467 71.361 10.51167 260.6453 15.44967 17.413 7.566333 938.454 20.73367 7.72 16.40267 80.658 7.913667 1.321667 14.42733 21.776 9.231 4.583667 15.246 15.437 65.235 64.46467 15.42567 15.32067 8.792667 4.512667 18.174 18.108 16.50567 12.19033 26.33733 19.81633 12.544 14.10833 69.556 40.363 10.23033 5.709667 12.327 14.04867 27.02667 14.676 6.723333 499.6263 12.226 21.74733 2.732333 19.28233 18.931 11.486 118.617 7.395 10.679 32.75133 7.087667 22.84267 7.66 9.647 9.294667 6.977333 14.08133 15.98533 84.71567 73.07533 2.032 6.174667 5.685 17.83733 28.212 8.274 12.023 9.925 13.91533 14.411 424.5863 16.38067 3.122 17.25667 11.013 7.516667 10.57833 21.41267 4.789 5.981333 13.76033 15.521 7.979667 7.807333 10.288 5.664333 23.04733 9.524 21.67067 2.503 0 8.352 8.369 11.173 8.836 28.223 17.55633 9.195667 5.992 3.596 9.865667 58.535 10.124 228.7547 15.28167 0.8883333 5.838 13.31333 21.40333 2.410333 4.98 72.50367 0.6243333 67.14133 2.327667 138.602 5.784 29.664 13.338 6.127333 7.374 8.525667 10.828 20.15033 7.045667 4.636667 8.232 3.51 23.05433 29.06 2.177 23.191 22.77967 37.02633 5.474333 9.638667 40.53433 4.895 9.153 15.31167 10.462 8.300333 8.412333 13.186 3.68 5.607667 6.318 0.4626667 5.468 6.257667 3.465 3.966667 9.302667 1.734333 5.763333 19.63133 2.115333 3.101333 4.385333 27.046 9.423667 1.195 0.668 5.190667 1.998667 0 3.158 0 5.458 1.586 2.939 2.341667 2.98 3.201 1.755667 0.093 14.50533 4.641667 4.132667 10.806 5.709333 5.685333 0 7.033 1.905667 3.141333 18.65833 23.73867 1.651333 0 3.513333 8.689333 9.475667 5.354333 2.409667 4.44 2964s num discordant: 0 2964s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset 2964s sampleA_mean: 539.652 558.1363 279.6767 526.2243 68.104 300.087 96.61333 691.0767 641.1777 103.6867 1406.461 98.85333 96.77733 620.406 478.7223 20.01233 251.019 536.193 850.6397 72.55133 967.4877 38.978 915.841 876.482 45.76333 866.6187 1005.984 1005.984 655.8127 733.6827 861.8193 81.319 213.4847 954.153 903.1557 555.952 1220.149 1784.069 551.9577 884.0843 98.448 509.7623 1117.319 20.97667 114.5207 226.9223 15.838 17.37067 57.579 2042.114 15.04567 409.1913 128.1763 5.762333 33.62067 70.24967 4.654333 950.0057 224.904 1690.757 103.9153 93.42833 360.2233 76.41333 260.666 1385.135 21.39933 504.111 39.57833 18.754 2.696667 866.9083 113.178 2466.545 1545.514 33.57133 1681.069 443.633 57.26933 16.51667 31.501 37.21967 35.44767 1094.775 11.583 40.61467 603.456 86.883 94.089 1834.914 1313.1 697.2287 237.8803 29.55 223.9227 75.48133 37.255 898.047 642.0663 2590.581 1584.902 62.50533 9.434667 121.0697 141.697 425.357 18.96267 7.212667 27.52967 15.73033 100.1173 71.78533 56.797 1593.583 13.98533 503.5693 94.847 50.14667 27.29 393.3037 44.93767 67.08167 660.21 617.7277 16.528 20.36667 25.55733 37.25567 35.29633 64.19 18.88733 28.45833 6.167 4.244 337.399 35.529 29.18933 443.3597 188.4693 1666.136 42.57533 2.713333 560.8327 129.326 39.67767 43.50567 37.942 22.92133 22.74167 7.601333 17.221 2.398333 47.34533 27.48633 63.58333 7.685 66.65833 31.92667 824.9103 1796.241 27.59267 759.571 670.486 7.282667 6.496333 15.08833 10.53633 43.09833 91.49933 5.017333 118.9327 23.33733 40.12067 42.16667 51.407 16.54033 77.21567 7.951667 6.546 123.0927 9.896333 65.027 110.725 5.557333 30.828 73.27533 22.627 15.92433 20.37167 6.300667 3.078667 2166.993 759.148 302.136 9.969333 14.71933 7.980667 17.48067 50.11167 225.547 5.802333 23.04333 16.27833 17.96533 48.27367 28.839 20.135 15.46533 251.833 354.6413 18.67133 134.6073 61.43567 74.00233 47.651 27.61367 46.75733 73.59667 10.30533 18.30633 325.5413 4.080333 1846.256 18.317 11.52 5.016 40.25467 46.23067 18.233 27.23133 40.23433 5775.202 24.63167 7.252667 2.280333 5.682 15.54567 36.11867 29.26167 14.91467 497.7577 93.21667 18.592 6.929 474.4033 3.595333 5.627 23.127 12.40267 25.71133 12.30833 13.78833 8.791 17.59867 3.451 23.09367 25.73033 49.835 15.18033 7.059 22.375 7.909333 43.83633 17.53667 6.745333 22.68433 20.71867 483.664 7.48 6.455667 3.586667 66.73133 9.767333 8.807333 10.12033 321.257 21.67167 28.26467 5.474667 7.963667 7.869333 2.154 2.177333 30.97967 14.33333 2.900667 34.33067 46.17067 11.93267 15.25233 35.802 9.613667 34.16433 756.3963 6.515667 11.312 19.73 109.3627 27.77367 1.919333 7.083333 7.107 33.21467 7.412333 25.208 43.001 3.139 44.97967 25.40433 9.824333 275.3867 2.592667 8.002 8.292 22.31833 11.98267 49.788 9.274 112.283 8.866333 17.85933 33.815 1001.993 48.562 4.745 46.73367 59.43533 1.292667 87.024 9.773333 0.838 4.281667 18.33267 6.812333 4.531333 13.64567 14.93733 8.395 25.089 16.899 31.12967 11.286 7.700667 6.527333 1.460333 6.248333 21.74467 7.782667 1.991 6.863 12.79833 15.01 5.931333 27.14367 2.811 5.733 16.64833 26.40167 20.81133 4.766333 15.57933 4.59 9.616 25.32233 12.443 16.66533 3.516 37.152 21.32033 11.40267 15.94867 48.976 2.433333 5.895 27.53867 30.75333 12.76533 4064.721 14.83533 8.631333 22.93933 8.077 5.415 6.091333 25.646 6.204 16.73 3.762 275.0887 20.261 1.851 27.83967 11.22367 5.558333 7.226333 2.068 95.166 21.06767 12.753 10.471 5.364667 12.36433 8.316667 11.22367 14.18933 2.682667 7.310333 4.341667 2.534667 9.105333 12.44167 1956.885 24.758 2.800667 22.17067 8.028 7.766333 6.686 3.200667 7.884667 18.23433 13.917 7.039 13.58 7.844 6.250667 266.444 4.361 5.740333 3.293333 5.615667 11.59067 13.71433 20.36133 2.243333 14.558 2.723 7.621667 20.74967 1.695333 16.116 11.91033 16.40367 2.411 8.497 9.510333 63.63933 10.72933 7.672667 8.578333 12.394 12.90733 5.630333 17.75767 6.380333 5.416333 6.524 34.157 3.294667 1.688667 13.22967 9.471667 4.676 7.431333 4.926 1.160333 6.778333 17.19233 9.436667 13.50467 13.106 5.332667 3.424 9.378667 74.79833 16.556 3.165 1.577 10.85033 2.194 6.625333 11.227 4.963667 0.713 6.521 11.94067 11.36067 16.303 26.291 9.694667 0.1093333 6.567 1.574667 5.421333 6.559667 7.711667 9.557333 1.288 7.325667 12.01933 11.758 5.177333 8.791667 13.65367 10.216 6.066 3.857 6.861667 2.758667 0.8066667 9.299667 3.09 0 11.994 5.422333 2.976667 2.163667 12.388 8.293333 3.109667 6.067667 6.829333 0.9146667 10.12333 12.14267 1.407667 3.468 3.979 23.38367 5.603 6.326 9.507333 26.67367 1.363333 10.201 3.493 6.512667 39.729 11.46067 8.411333 3.822 15.47733 19.73733 3.680333 1.911333 4.482333 3.736333 11.24533 15.75333 1.302333 6.395 8.805333 0 4.293333 3.27 8.445667 0.409 4.053 1.547 3.301333 6.606667 7.337333 0.248 3.051 0 7.585333 0.7683333 2.517333 2.745 2.219333 4.638 3.268333 4.765 2.330333 4.127333 2.818 1.897333 4.196667 2.605 5.581333 9.374333 6.813333 4.484 2.467333 8.839 148.8903 3.489667 2.550333 2.692333 3.090333 0.4346667 1.384 3.043 35.57467 3.162667 1.252 0.01 7.634333 5.001333 4.695333 4.126 4.009 0.3906667 0.6643333 5.633333 1.870667 4.744333 0 1.153667 5.019333 3.021333 0.724 1.344 2.011 2.448333 12.573 1.351667 4.724667 4.196 3.398 1.169 2.056667 7.756333 2.678 17.98467 1.122 8.025 35.02267 0 8.504333 5.509667 0 8.218333 0 1.184333 2.578333 0.9123333 3.328 8.963667 9.984333 2.877333 0 1.56 0 1.469333 19.30967 0 3.570667 2.844 1.863 4.313333 3.484667 6.267667 2.573667 1.102667 10.61867 3.682667 0.989 1.980333 11.52467 5.264 8.003 1.637333 4.572333 4.102333 0 21.42967 3.945667 3.773 2.242667 0.768 1.994667 3.393667 2964s sampleB_mean: 6464.644 7520.41 7779.492 6944.853 1492.051 2827.345 1331.648 9939.373 7181.47 1438.471 10849.9 2550.414 971.4367 11165.49 5346.478 1076.978 2449.757 3982.392 6705.697 1007.03 5874.642 347.4017 6156.043 6887.084 440.9727 5515.698 8614.152 8614.152 4540.328 5036.385 4809.412 973.0083 1506.715 7405.14 5974.238 3104.744 8313.711 8625.824 3325.992 5589.41 819.1427 3398.294 7596.105 303.273 876.8277 2510.784 501.0717 217.5877 512.042 12136.75 147.2877 2649.173 850.5097 155.6753 318.3057 493.2167 193.995 8726.054 1237.565 11956.17 803.7297 1192.947 4624.974 395.6523 4978.607 10695.83 341.9023 3101.543 381.4813 176.1237 324.8553 5311.835 1781.496 12803.12 9160.812 286.7303 10005.84 2806.072 644.756 721.2523 297.5633 337.5617 722.7793 7921.826 188.059 510.9113 3043.903 880.4753 592.331 11807.78 8077.68 5150.462 1147.187 178.331 1388.008 369.4417 568.9407 7137.863 4181.758 14596.83 9231.562 820.1 227.1767 1183.775 624.4283 3135.76 165.5147 98.27667 374.99 126.265 464.656 437.7077 498.566 7646.521 340.8923 2069.238 501.203 223.6213 347.1993 2813.865 330.2803 497.3057 3606.195 3477.406 210.5073 237.9167 229.8227 636.1717 265.4807 303.588 234.8707 464.25 59.968 88.77667 1727.754 277.6277 568.3683 2899.79 1232.959 7998.991 221.5063 135.6287 4052.112 784.5 437.8937 242.2357 198.0453 177.0987 151.089 204.598 209.5997 136.0917 309.0137 318.668 366.6233 53.11833 365.304 205.964 5402.498 7391.381 248.7967 5955.872 3497.592 304.1167 96.888 102.4913 224.959 365.9053 383.3883 183.432 954.507 146.225 244.213 228.616 346.0203 159.9217 617.5097 322.6313 124.821 566.3103 130.7987 744.834 473.468 41.92667 221.3943 376.801 257.8713 171.415 169.5693 58.786 363.4697 12057.81 4659.391 1314.765 76.629 93.961 79.78767 361.7567 208.997 1374.415 87.30767 227.959 201.1477 153.6373 297.5293 204.0893 171.2443 88.84733 1538.062 2636.168 84.19433 794.7277 261.1813 434.0653 219.043 146.7367 306.1523 324.095 254.0923 728.6047 1485.8 204.688 10466.26 92.66933 139.8577 133.1137 243.0527 199.25 134.7863 396.4167 259.974 31019.62 102.9103 55.56067 91.93733 190.3363 196.2657 210.276 120.016 307.597 2478.864 434.0367 160.6447 65.82467 1924.887 92.04867 148.3807 125.9207 110.12 217.828 186.3673 112.8707 92.801 102.8277 85.369 332.1927 109.1297 317.4007 106.9733 118.4783 162.353 132.86 279.8187 88.724 115.6383 145.871 94.855 2983.166 53.67933 163.2497 107.6607 288.2643 63.51467 44.52667 104.7473 1573.052 91.36867 130.4647 129.359 189.81 49.84633 38.50333 132.997 155.6507 198.031 56.084 189.876 241.8647 92.14267 138.9953 221.9553 141.1233 383.105 3680.324 240.9067 166.719 108.0163 502.0593 219.1713 79.23 51.48067 72.27033 147.5143 327.728 434.5497 251.6407 293.4293 506.512 150.83 165.6487 1190.783 199.5333 72.04033 71.07333 188.654 54.17467 217.945 109.0163 446.5917 101.2043 89.19033 264.5573 6554.638 404.8233 177.6103 244.312 451.6893 65.022 391.7213 94.036 381.073 160.461 125.6427 175.727 102.4957 142.4997 114.7247 91.96267 313.5353 80.658 160.033 139.4217 55.31033 138.7943 66.28233 65.14433 97.74133 67.32633 88.20067 48.662 71.95633 75.13167 98.59367 111.3283 42.94067 79.15267 112.4907 143.6177 138.8203 82.77467 83.32767 57.92467 92.10033 147.9097 55.42833 92.673 615.4837 329.0943 177.7223 86.82867 117.3687 272.869 176.1103 72.229 123.7103 205.2823 65.265 23095.85 63.39167 98.42267 143.2053 52.40167 36.84367 30.305 189.338 68.93667 70.82967 136.3853 1768.526 97.67333 59.07767 126.6667 54.697 78.15767 63.519 54.28 629.935 114.413 98.25867 51.40267 33.64933 61.75633 62.202 47.69867 106.367 64.48933 61.927 58.84033 31.92033 44.59133 59.70833 12433.72 108.9977 66.58633 101.2333 37.13833 92.91767 92.354 67.97633 69.31567 185.3687 75.314 59.309 205.7273 44.65167 578.1793 1437.071 565.0517 49.55567 57.289 71.83833 56.87433 80.30267 89.473 25.16133 84.09433 64.96333 39.14833 97.91867 26.105 359.4497 59.017 91.34767 20.836 37.861 40.01867 269.8203 43.553 36.83567 51.20733 63.275 74.47967 28.11233 72.092 57.89033 31.81733 29.19933 180.145 17.67167 27.42533 92.58367 53.35367 45.43467 42.02167 86.666 29.412 38.239 71.77333 50.94033 70.23367 70.48667 24.105 36.129 51.208 654.0063 104.9537 16.98933 21.31667 60.39433 38.35733 36.76167 100.9357 24.998 60.909 31.64467 49.809 60.34067 558.288 105.9517 44.80233 58.52433 40.58467 374.3023 40.88467 65.641 37.373 43.199 23.09333 49.184 58.53467 83.02567 42.55233 67.40867 58.72433 49.53233 44.57067 46.01667 74.76 37.18267 94.084 39.439 32.39167 41.25767 77.42067 28.99667 23.031 323.135 82.208 95.03067 52.62167 48.09067 63.80367 61.049 52.59533 118.5717 17.978 22.795 343.3797 275.1827 284.8557 25.818 38.56967 170.258 33.71767 45.68133 22.759 134.3513 170.7703 147.841 56.735 19.01033 64.17467 89.41967 28.08767 19.87967 50.66867 50.351 59.187 63.14133 63.43233 35.30367 40.58733 17.20333 21.37133 21.26833 72.57967 40.14133 24.42933 27.15533 28.618 33.96667 80.83067 18.746 19.069 101.7453 57.38933 12.81233 26.59233 25.20967 16.69733 39.557 134.6853 46.573 16.53733 31.40267 81.03933 17.666 18.67167 16.98933 31.359 50.767 34.963 38.06967 82.00433 43.21967 541.9867 79.93733 17.60767 21.58933 13.31667 9.165333 45.292 15.914 200.7123 13.12667 16.692 16.39933 62.14133 38.21633 130.2143 18.98967 21.925 17.79667 12.13567 79.05433 125.1613 23.01233 29.38867 58.21167 42.533 51.753 23.8 10.878 70.339 37.33167 122.654 8.173667 24.04433 37.97 14.291 55.27767 11.24133 37.89133 23.558 67.874 10.06533 43.66433 139.358 33.81667 37.642 24.348 11.09467 69.305 8.385 47.25833 28.28967 17.76433 20.035 63.401 48.78233 12.62967 35.64 22.82667 9.080667 11.03933 92.552 1.073 15.776 13.166 45.16467 23.05967 37.25433 24.88967 22.41933 27.504 45.16833 22.33433 22.85333 12.07167 76.51933 19.075 34.98133 14.71567 21.97667 23.06333 11.718 133.2117 26.364 18.868 19.56367 17.268 11.69767 23.021 2964s num discordant: 0 2964s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_37-UP.subset 2964s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test. 2964s sampleA_mean: 6030.232 1681.385 1407.266 5797.692 1833.283 20787.35 1046.9 2191.464 1326.5 4954.434 5495.505 4913.275 12222.46 4191.816 2602.336 2635.243 944.0123 1512.754 1013.064 1371.045 982.539 559.8297 335.7477 637.4673 1272.664 1265.232 1751.765 1445.705 521.84 887.2083 1532.142 326.0873 1233.492 2002.536 1939.628 3549.085 1593.001 4784.861 562.1487 470.179 1262.588 810.3883 1718.763 5645.434 499.8527 1037.645 388.648 405.4877 1707.219 581.2863 3468.578 647.4437 925.3123 178.6107 258.5643 933.0403 1031.742 371.296 1348.496 393.785 116.9527 15024.4 999.5363 335.637 335.2157 1088.069 564.1773 1753.538 405.9907 533.844 460.3903 1091.041 425.4187 104.2153 4713.887 1933.215 154.4447 1640.267 387.8127 620.238 923.62 296.1627 36600.33 1816.62 2446.14 825.5967 838.8547 1291.39 194.6923 1656.826 298.6353 1179.723 521.2813 344.3147 604.7417 2017.126 159.0503 2237.79 531.0443 876.645 581.914 772.306 610.589 494.789 508.1423 872.2057 1707.261 664.8137 252.8977 337.767 1547.728 337.406 150.8137 133.8673 1030.087 568.889 482.3557 1434.927 1120.621 244.4597 234.695 233.2683 363.4713 5637.134 176.112 480.5827 1756.628 147.324 168.438 349.218 356.3497 378.0157 594.819 762.2617 2891.881 244.753 272.6143 85.82433 350.3023 1125.723 146.7767 210.486 201.4867 198.9307 114.485 156.591 182.1447 435.0017 991.437 432.0453 563.9263 176.9843 241.211 322.1607 368.628 219.039 1412.697 114.123 5395.606 209.749 407.6713 122.4237 1198.79 502.9777 71.71033 323.746 617.5563 310.3323 116.1613 99.45067 300.2583 240.267 719.3537 125.2723 854.0897 590.469 164.083 109.0817 1315.006 100.0037 89.249 89.41233 177.4467 189.715 97.82467 207.939 437.1223 122.591 770.6237 198.061 207.397 183.172 316.5037 128.0267 324.5383 91.99833 354.7773 389.129 164.5937 127.1483 60.22767 328.3217 161.1783 567.2883 63.90033 665.289 407.805 105.1747 132.971 734.0483 62.56033 1229.376 335.4993 300.3533 294.269 168.189 199.325 104.0613 78.31633 206.046 84.98533 132.1053 499.693 160.8853 210.2437 129.574 122.177 87.49733 250.2393 98.94267 236.6537 471.4763 115.35 519.577 173.3993 172.982 124.4867 181.09 2465.916 59.607 280.7067 60.025 81.80933 154.7137 562.891 291.7607 421.348 169.0567 721.5107 93.672 62.65367 310.3963 94.07567 76.27033 66.11467 55.68233 94.133 98.85333 363.302 278.785 603.3643 113.344 90.65667 105.6967 171.9977 136.4807 156.8307 40.38733 204.4367 3561.451 212.7377 214.102 93.57967 46.29267 62.81 103.573 80.98433 78.67633 305.3177 304.6523 66.544 2036.308 77.01533 53.23867 66.88467 52.74467 1557.898 120.7347 1505.046 95.84833 135.433 51.06833 471.7457 38.966 781.6647 38.21567 54.279 86.272 64.515 35.384 32.07433 32.60533 194.3693 187.0867 971.5327 50.39 56.34967 47.40267 97.46133 3088.486 1606.153 33.614 26.77667 56.42633 47.17133 71.85 27.49133 69.30367 233.2737 158.4977 144.1087 407.7717 74.26433 44.67767 73.156 31.01767 131.435 87.15633 40.76933 44.27933 630.4887 71.55767 86.26767 30.31033 50.27133 49.19267 40.022 93.98167 16.066 42.259 51.916 6075.931 751.6327 69.90667 37.93767 101.362 34.524 35.92467 354.898 82.45067 37.746 425.4893 171.2653 280.1693 42.52667 56.986 58.77867 56.78633 47.12267 51.36633 114.1953 38.41333 26.93367 84.101 58.726 163.5027 42.42 27.86967 26.74467 52.054 70.90433 48.80533 41.489 141.5087 19.36133 34.55067 142.1963 32.87767 19.379 43.001 51.68567 42.69267 69.761 52.49167 45.27567 115.2073 7.951667 27.10933 51.49667 84.52867 4534.064 269.428 38.71367 209.263 24.04867 59.42133 36.44033 31.80833 20.94233 28.112 28.092 26.72567 31.895 32.359 36.69767 20.61433 45.48233 43.59833 38.467 132.0313 66.32833 59.42267 33.66067 20.87967 22.01133 13.58767 13.46233 14.442 19.87867 45.49933 24.69267 23.94367 496.4993 27.92067 56.72833 23.62733 73.985 12.36533 40.90567 13.02633 28.60833 14.06933 37.072 23.51567 32.296 27.81033 10.913 30.83533 18.52533 26.52667 29.40667 36.76933 28.27267 87.54867 27.07933 20.89067 41.65 13.554 18.73767 26.41767 15.976 44.083 16.59667 20.15333 23.038 45.54267 18.127 25.49633 27.188 22.07333 36.86033 12.43333 27.52167 68.59733 20.84167 2964s sampleB_mean: 71.58533 34.85667 61.93367 190.2367 18.24467 1576.856 21.734 67.15133 46.38933 175.0553 10.731 231.01 644.6073 162.736 28.83167 149.0183 40.62 120.2997 20.73967 20.785 38.35033 38.834 17.87533 9.523667 122.321 70.315 11.541 39.02467 15.272 11.73133 216.263 34.29367 131.954 60.698 191.4833 54.76233 84.69133 176.7203 41.809 14.071 5.897667 97.40133 167.6013 1058.536 10.32667 154.1127 51.789 68.43533 199.414 69.84367 143.0547 18.007 167.5307 17.35367 20.43633 82.944 146.7283 11.974 62.01667 46.20633 6.833333 126.2827 52.632 31.756 18.10167 85.388 44.774 290.869 33.76633 99.03833 86.94433 78.63867 62.69867 10.803 184.242 91.85267 6.593 172.0003 32.09667 5.31 94.25133 21.86767 312.258 3.02 327.4777 138.9923 157.5777 15.897 11.08667 70.838 29.81633 120.642 34.63 48.44967 135.326 263.582 29.81667 176.0093 59.39767 96.643 81.38067 52.029 119.8197 7.353333 111.2203 151.9077 274.274 138.5447 13.45833 57.83967 296.326 44.574 13.40767 18.47767 236.2837 98.93967 78.18267 147.5103 4.916 33.99767 6.119333 22.66633 18.10667 585.796 10.14033 81.65333 288.293 29.03533 24.10267 81.69867 45.153 60.40333 21.75133 60.149 107.587 4.303333 14.93967 16.697 68.39567 239.1367 9.162667 33.16933 37.04267 5.075 12.202 25.95767 31.26267 18.98533 228.12 62.152 71.425 33.04933 52.859 17.25433 77.462 31.115 4.947333 5.291 4.892333 6.52 77.499 7.044667 112.516 2.201 14.63133 40.80033 35.93933 36.04767 26.55867 11.37767 8.328333 46.24133 131.7207 22.86333 10.01733 19.323 29.20433 9.454333 252.1407 7.705667 5.086333 11.83333 41.19767 31.045 10.11133 42.20867 64.78833 5.435 76.85 43.10367 22.379 41.53733 66.14267 15.958 44.73367 21.33367 81.672 52.96867 15.18533 28.43733 12.457 46.83533 33.53433 5.055333 12.78767 5.982333 80.735 20.32033 21.17867 1.413333 9.876 252.5313 2.999 55.72533 60.023 37.84833 11.36967 14.93967 11.56533 27.23467 11.13 28.67333 5.957333 19.13967 3.039667 25.094 3.384 16.72967 50.52767 15.63733 53.45667 103.8797 24.55133 68.06833 41.26233 27.607 21.97267 29.328 192.615 9.053333 57.499 12.56167 6.152333 36.59667 92.249 49.06433 77.08667 24.19267 64.61967 16.52467 14.59467 1.439333 4.922 17.05033 3.929667 8.892333 13.001 16.70467 72.445 38.40433 32.20767 26.43 15.84233 19.338 26.382 23.92933 3.080667 7.813 41.21667 52.72333 22.53 49.04333 15.72 6.808667 11.71167 1.620333 16.686 2.519 58.95767 72.39567 15.178 456.8783 15.967 9.581333 10.61567 3.457 221.51 4.436 300.8857 20.181 30.64367 3.424 63.54133 6.782 0.8923333 7.134 9.956333 4.478333 3.776 2.932 2.596 6.225333 41.753 44.787 161.046 8.024 9.696333 9.795333 19.69133 8.807333 129.8027 5.698 6.056667 6.818 10.08733 15.87967 3.111 12.49533 47.94933 24.952 22.72933 79.67267 14.317 9.568 3.546 6.028 23.79767 10.136 5.855333 2.343667 144.8737 6.153 13.70767 5.053 9.387667 9.898 2.558333 11.88467 0 6.709 9.442 603.3247 131.0337 4.551667 5.482333 8.861667 6.474667 5.451 10.47367 12.136 7.286 38.81867 6.163 10.048 8.245667 3.947333 13.348 5.819667 10.034 10.76167 25.736 0.77 0.388 9.684333 3.721 30.05333 5.672667 5.932 0 9.460667 15.06367 4.762667 1.601 5.704667 2.312667 4.229333 34.28533 6.930333 2.445 6.886 11.101 6.758333 16.034 12.28333 10.75867 0.8253333 0 0 3.487 18.601 1.982 60.65633 8.657333 9.86 4.175333 8.966667 5.916667 5.966667 0.597 5.907333 1.379333 4.023 5.972667 1.994333 2.795333 2.932333 4.818333 10.182 2.289 26.49267 2.695333 3.923 1.628667 0 4.613333 0.3683333 2.201333 0 3.583333 3.518 0.911 4.885 96.05 2.298667 2.356667 3.766667 3.183333 0 4.880333 0 2.238667 1.082 7.471 1.805 6.506333 2.091333 0 7.344667 1.954333 1.173667 3.284667 2.515333 0 11.32267 0 3.392 2.037 2.414 0.7583333 2.759333 3.673333 8.528 2.582 4.356 0.831 4.943333 0 0.774 3.599 3.673667 4.728667 2.062 2.479333 7.661333 2.833333 2964s num discordant: 0 2964s validating: Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset 2964s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_37-UP.subset) passes test. 2964s sampleA_mean: 96.61333 15.04567 103.6867 88.57 224.904 7.685 72.55133 6.167 21.39933 15.838 509.7623 36.11867 68.104 803.1917 31.261 141.0787 102.2703 503.5693 539.652 655.8127 30.97967 76.15267 478.7223 28.64033 98.448 504.111 121.0697 40.988 526.2243 37.21967 558.1363 20.01233 1275.026 578.8703 279.6767 733.6827 337.399 409.1913 18.96267 291.1757 300.087 125.9483 915.841 96.77733 16.51667 88.20633 5.762333 763.5533 55.26267 903.1557 46.17067 45.412 57.26933 81.319 641.1777 16.54033 443.633 697.2287 31.92667 78.96333 31.501 40.83233 354.6413 850.6397 40.27 620.406 113.9973 20.97667 14.71933 24.615 4.654333 7.252667 10.53633 25.78433 33.57133 11.583 11.22367 9.434667 7.282667 47.34533 22.74167 7.212667 43.50567 237.8803 26.208 115.4593 50.11167 188.4693 425.357 35.44767 26.51267 2.713333 31.97667 33.62067 5.415 223.9227 110.725 209.5917 4.244 23.127 23.33733 81.34233 25.605 87.317 106.1753 29.55 225.8327 20.36667 47.036 19.92833 159.4173 87.42633 23.94067 2.398333 43.09833 28.26467 691.0767 71.78533 91.49933 12.94133 37.27233 103.9153 18.754 16.528 642.0663 40.25467 57.46833 9.896333 670.486 18.317 7.963667 7.980667 51.407 22.51133 171.0287 34.135 15.54567 55.73 16.899 11.52 89.987 27.29 25.55733 13.98533 56.797 21.51767 759.571 15.92433 4.080333 18.88733 66.65833 5.557333 64.82733 23.04333 24.63167 15.73033 5.627 30.80767 25.208 26.715 65.027 18.76 9.969333 17.48067 30.828 48.562 5.017333 19.11967 3.451 6.546 13.46667 5.630333 6.745333 16.27833 86.883 9.642 26.67967 17.96533 24.758 8.791 42.57533 27.48633 393.3037 27.59267 8.807333 443.3597 14.063 29.18933 22.68433 241.785 22.31233 7.059 39.57833 216.0503 2.696667 497.7577 15.08833 7.909333 39.67767 15.09333 103.2833 15.18033 3.595333 3.941333 75.469 15.01 5.682 17.221 4.281667 142.0663 11.438 27.94767 5.016 5.474667 12.39433 37.152 12.993 37.25567 3.586667 321.257 3.420333 23.09367 2.280333 18.62433 13.08133 12.98 11.312 2.154 31.32 52.084 62.50533 11.29367 50.469 7.844 2.068 6.496333 32.849 35.29633 44.93767 1.292667 27.83967 37.255 5.802333 20.135 20.992 6.819 6.980333 22.93933 6.515667 79.21967 22.17067 17.19067 6.919333 4.371 8.162667 260.666 26.75667 21.116 11.22367 13.78833 20.37167 10.216 2.243333 50.97333 4.59 47.42233 7.107 6.674 18.233 49.835 6.929 3.078667 28.45833 6.300667 11.93267 22.752 9.507333 118.9327 10.30533 8.316667 20.74967 7.354 8.497 33.50367 55.59767 6.812333 1.919333 5.931333 9.735667 20.16567 7.48 28.057 30.424 12.753 10.95167 18.30367 5.733 2.433333 2.219333 20.261 23.67567 16.556 6.455667 2.811 4.156333 19.73 3.139 27.23133 22.996 1.460333 9.767333 12.36433 84.312 3.200667 8.077 9.557333 16.40367 19.921 1.991 14.78033 7.039 77.21567 26.291 44.996 3.043 22.627 1.577 5.895 2.177333 2.330333 4.531333 11.286 4.745 8.002 2.550333 4.341667 4.766333 11.227 40.34367 2.900667 5.177333 9.773333 2.534667 3.468 13.65367 6.527333 7.310333 28.33667 14.06433 44.07433 17.85933 7.050333 25.40433 35.802 8.578333 12.40267 14.22267 11.817 5.615667 33.01633 0.838 7.412333 6.524 17.692 54.75267 9.613667 2.592667 6.559667 9.824333 5.364667 1.911333 8.393333 5.720333 74.79833 25.32233 15.64 8.043333 10.38333 28.43467 18.33267 16.303 4.963667 11.59067 27.77367 7.884667 8.631333 8.866333 9.616 7.555333 0.713 25.361 10.12033 15.57933 7.216333 4.676 3.857 17.332 5.740333 42.16967 6.910667 14.16 21.06767 12.76533 2.723 7.431333 13.23767 8.403667 8.173 11.097 7.672667 7.163 2.411 11.21733 18.93367 18.30633 57.61633 3.424 30.75333 6.066 1.688667 5.416333 21.69333 0.1093333 11.36067 5.332667 7.394333 14.91467 44.679 18.23433 0.6643333 39.729 6.204 14.94733 6.983667 13.22967 20.36133 33.10033 1.160333 25.089 13.50467 6.248333 6.863 0 0.7683333 7.083333 1.288 2.976667 0.3666667 0 1.469333 0.4346667 5.558333 11.994 3.762 1.695333 21.88733 6.592 10.201 3.162667 1.162333 33.815 9.744667 8.395 1.252 34.16433 3.294667 9.471667 2.163667 3.541667 6.380333 2.682667 8.791667 13.58 6.521 0.248 7.168667 1.715333 8.805333 1.363333 3.09 0.485 11.758 7.621667 0.8066667 16.06567 7.585333 11.40267 7.601333 1.448333 1.444 18.94267 10.85033 7.325667 5.596333 2.844 6.625333 2.745 8.198 9.752333 5.581333 6.861667 12.67933 1.122 13.88733 2.605 5.057 4.058 21.32033 15.09267 0.9146667 8.038333 6.067667 4.064333 8.293333 5.264 53.09233 3.418667 6.752667 6.567 3.292 0 0 23.38367 3.109667 1.897333 3.765 0 1.302333 4.196 2.922 3.822 7.766333 3.090333 12.14267 4.638 18.91833 2.14 2.715 5.421333 4.926 8.351333 4.053 8.255667 7.195333 6.754333 2.517333 1.851 1.407667 2.474333 6.512667 4.325333 3.425333 0 3.122667 1.281667 1.574667 3.273 16.116 5.603 2.883333 11.89067 1.351667 5.686333 8.223667 5.060667 1.981333 1.649667 2.818 161.101 1.994667 3.979 3.179 0 0.5473333 4.765 0 3.219333 6.893667 0.7146667 4.387 0 4.989667 4.009 1.769667 2.194 0.622 2.877333 0.4176667 6.813333 0 0.2473333 0.409 0.676 3.493 2.414667 12.75533 7.337333 4.695333 1.547 3.696333 0.9123333 4.572333 1.992333 2.800667 3.293333 0.939 3.733667 2.275333 11.126 2.310667 1.492667 8.773 1.980333 3.398 1.637333 36.09 2.692333 2.337333 3.319667 7.756333 3.403333 1.776 0 1.089 3.077333 0 2.577667 3.570667 0.4253333 0.989 2.663333 4.451333 1.344 3.992 2.347333 8.963667 1.544333 1.576667 3.021333 1.844333 0 4.123667 2.259667 0 0 5.287333 2.573667 4.611667 0 3.945667 4.385333 0 0.8176667 6.45 2.448333 2.962333 1.941667 0.7693333 2.578333 1.870667 1.324 2.192 5.509667 8.504333 2964s sampleB_mean: 1997.885 370.6363 1889.849 2830.628 3005.897 339.544 1611.849 266.1853 1524.761 2001.57 4325.944 2415.454 856.342 4759.337 809.747 1374.611 2786.993 3179.415 3396.666 3693.07 566.031 759.8243 3249.388 686.1263 875.9707 3216.203 2237.994 1440.661 3330.022 394.7987 2922.537 344.6643 5398.857 3756.434 2471.048 3620.716 2883.64 2374.126 211.0497 2047.901 1235.974 606.0663 4427.58 485.2353 736.2793 476.768 90.55133 3709.705 953.5553 4251.336 768.1787 241.776 556.5843 630.4883 2990.729 253.343 2376.446 4895.859 300.4817 439.0257 240.971 562.3953 4198.375 3423.331 310.312 3616.512 461.5343 140.997 140.0233 166.0277 105.6647 118.7197 285.4657 378.7327 193.8653 144.7763 142.302 146.4013 437.971 298.0877 171.3853 79.82167 269.2717 925.7747 265.6093 760.6557 267.723 1094.26 2436.015 421.1887 574.6353 149.84 279.329 189.6917 208.1393 1049.838 511.8627 1034.454 73.643 199.6 167.053 401.21 255.2837 365.2543 731.863 127.811 1012.972 165.0047 203.65 79.65933 927.6743 434.556 166.8767 112.4467 341.4467 194.996 3650.525 280.2643 357.7387 116.6347 218.6657 444.0447 105.6257 120.8233 2890.802 332.1813 290.862 135.609 3849.83 98.13967 472.5113 87.31133 321.7517 155.4747 878.6043 320.243 267.5577 274.3337 133.069 192.3193 683.449 212.3977 160.4317 164.205 366.123 96.142 5152.482 133.1023 348.3133 138.4137 287.485 38.85333 255.8583 189.5857 127.943 88.38 130.9923 125.2547 366.0723 178.71 699.6877 132.628 58.79033 263.798 175.8867 692.2687 132.7817 120.8867 120.2137 84.91167 143.3147 55.55933 90.86167 177.3257 404.5893 90.957 178.5933 115.1327 193.4727 97.3 162.5713 189.0233 1642.015 149.819 40.32533 1780.032 75.75133 259.148 150.3183 1082.98 161.1673 109.1813 153.0033 842.3293 42.12067 3067.808 62.39367 118.3287 254.1857 253.0167 443.3713 90.116 71.08433 31.73 428.623 117.2697 141.5657 123.721 317.0973 568.8347 160.1683 162.3163 96.602 140.1517 53.59967 609.5917 194.1133 260.6683 87.15567 1547.523 58.96367 216.949 68.593 83.573 91.18133 74.99667 177.183 39.998 148.7563 224.5063 382.3843 59.23867 286.777 92.43267 205.6727 48.27933 151.599 136.5493 207.045 67.006 168.0607 229.5497 58.06633 116.5553 87.012 85.78933 67.408 220.7547 165.4787 496.8353 184.3507 132.4173 92.061 51.73767 69.18967 1395.183 213.8997 95.749 74.632 88.725 101.0153 195.2947 65.65667 232.1147 60.63 252.983 69.947 59.629 107.4287 351.08 49.419 105.0843 186.8647 33.62833 68.66267 194.3873 109.6237 460.2323 140.2763 67.72533 145.5417 41.93 72.854 143.872 303.08 166.5273 59.379 131.585 91.509 102.0507 57.40167 218.8733 124.6713 134.7907 127.5543 150.3003 96.957 382.0493 151.719 140.8457 143.433 385.176 103.81 57.69533 87.65567 78.48367 126.504 195.6537 136.4563 60.04567 45.994 71.93733 473.3597 125.4973 53.67167 96.76 143.607 118.1207 80.46333 96.91167 123.938 323.664 199.317 231.7267 117.851 110.8577 83.61967 61.29533 81.26567 119.8297 82.67333 132.2 120.4613 48.91 156.2033 76.57167 79.68 240.6073 161.956 32.967 133.338 67.53533 43.412 64.25433 108.7427 85.55767 80.51633 174.409 69.52233 177.785 77.092 36.76567 100.6683 142.4753 77.97333 63.03733 71.81167 53.655 93.48367 183.9787 104.978 136.346 35.42167 127.9993 209.961 62.05533 71.74267 183.3313 84.66667 34.301 72.596 51.723 39.086 1621.57 114.4257 89.57667 303.0437 71.949 188.4637 88.05067 1604.347 47.35667 53.014 123.1273 76.68167 90.91333 53.52367 63.84367 29.627 136.4467 98.33933 55.85733 78.28033 36.70233 65.56833 83.324 68.32067 38.799 178.2697 27.296 76.47533 90.31267 61.12667 69.599 51.13867 62.81267 71.28167 50.22033 47.47333 40.14733 293.9087 22.85467 73.193 100.608 188.329 230.7707 34.95467 151.883 57.43267 36.13033 37.65433 311.329 161.9667 76.577 27.176 47.69067 77.38367 191.3687 159.7823 84.001 280.2713 43.65367 138.9263 37.29667 84.28567 84.57567 137.8557 28.55333 149.342 62.27133 30.21933 30.35033 22.75467 96.94267 27.671 30.70733 31.70567 36.6 251.767 68.608 177.154 56.562 120.206 57.43367 19.45267 106.615 48.224 55.77667 29.26867 61.53933 131.6793 68.67667 42.95633 36.72267 133.2 14.628 49.472 423.253 33.21433 79.551 27.28933 61.486 126.4583 35.098 82.68433 31.52433 36.53367 49.36433 41.03967 37.55767 76.24933 150.4293 31.972 80.36 84.252 43.97967 50.05667 31.336 127.1577 59.38567 176.0977 48.89833 42.60033 40.13033 35.499 25.97433 39.59267 32.39667 42.28633 48.22433 79.067 61.23533 27.11633 69.843 33.399 34.77567 27.94833 91.86567 61.76067 61.21367 38.139 45.60867 30.03567 79.87367 44.01933 356.891 32.58033 65.255 33.70267 33.73067 86.78467 19.23067 329.1877 44.45533 21.83433 28.714 7.434333 130.8803 56.93233 16.267 15.205 52.33733 16.67967 183.6017 46.144 107.6573 22.669 33.473 27.93333 58.25633 58.12767 17.84967 49.72933 30.596 37.849 30.23233 13.23833 12.861 33.19833 98.03267 22.413 15.277 7.787333 15.02733 20.92033 84.23433 18.09167 95.334 186.3597 28.15867 106.4977 14.83167 21.914 117.513 26.27467 49.82833 18.50433 67.063 885.105 18.55533 93.36767 20.35933 31.383 28.44433 34.77033 3.268 29.242 28.39433 73.018 21.34167 30.69133 65.14467 26.188 27.04033 16.95033 17.43 15.656 19.80633 27.944 18.48833 19.36667 18.61167 31.89 13.99333 38.715 66.67867 77.94767 106.1883 19.614 26.23633 24.30433 37.429 30.54067 22.274 13.36767 23.73133 70.27367 17.236 80.966 31.73667 20.05633 78.66133 12.443 16.01333 13.41633 166.674 17.96033 23.945 14.817 38.17233 18.03233 35.44867 25.41533 15.25033 28.101 14.14033 17.898 16.27233 13.18233 29.174 15.33767 32.61467 13.94367 16.55367 12.703 62.61533 28.76267 17.502 46.892 14.40533 26.512 22.969 13.60433 15.03767 40.46467 25.09 20.55233 22.38467 18.481 35.23233 18.28267 12.082 21.75 62.73233 39.09833 20.87567 18.62033 17.31067 15.10167 48.44967 11.96033 12.63367 20.713 37.68333 2964s num discordant: 0 2964s validating: Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset 2964s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test. 2964s sampleA_mean: 4624.974 1506.715 1636.976 440.9727 1101.219 876.8277 12470.43 2550.414 1781.496 512.042 324.8553 871.6373 707.8263 493.2167 834.608 177.0987 217.5877 347.4017 768.306 645.4617 339.8283 850.5097 3211.031 621.286 198.0453 514.415 411.447 501.203 1098.868 3078.184 222.09 189.5647 95.89333 510.9113 620.017 646.6133 429.5973 224.469 306.1523 1192.947 474.0487 1003.238 1494.298 900.1817 856.7063 374.99 244.213 623.5437 173.88 689.711 237.177 211.7417 646.864 204.598 378.627 132.9247 257.3087 198.031 2373.043 97.24867 166.336 138.8203 109.0163 153.4527 116.0807 661.7387 194.0203 189.876 151.8027 188.654 149.5763 75.79967 328.0923 276.1017 506.512 272.869 161.0497 202.739 37.50533 92.354 215.8967 194.2893 2633.716 103.0963 278.7853 54.95833 112.168 175.2467 53.598 63.519 59.07767 103.6453 100.247 214.853 55.41567 91.645 114.2777 131.159 374.3023 72.98133 499.6263 46.03533 88.61667 45.62033 55.17567 615.4837 106.367 63.24267 80.30267 583.86 82.208 51.208 322.6313 160.284 58.90833 565.0517 112.6127 103.33 541.9867 43.62667 30.70067 39.745 75.16967 36.49633 46.59433 94.455 99.289 227.2843 170.258 189.338 137.7607 40.44433 39.40267 39.44033 578.1793 52.59533 63.80367 28.455 83.27833 32.245 25.087 69.91033 28.618 41.25767 13.208 82.00433 40.18733 29.69867 27.874 37.18267 42.52533 50.351 43.80133 19.68333 35.30367 72.777 50.66867 72.57967 81.69967 124.9103 25.539 50.767 36.466 24.83067 134.6853 7.618667 75.28167 147.841 25.74867 45.16833 31.79067 31.40267 48.78233 23.51433 33.46233 79.93733 63.05533 31.89567 63.71067 18.93167 36.90167 23.01233 28.191 29.06367 59.28433 38.06967 76.51933 18.83133 22.33433 58.47233 19.622 18.868 19.09633 68.14433 69.305 101.7453 48.16367 26.44133 22.32333 29.71933 92.552 57.61033 27.69933 23.021 56.21533 28.387 43.573 45.292 26.81733 20.62167 122.654 52.69467 48.025 72.11233 24.891 67.73133 22.708 27.838 55.27767 49.08533 24.47467 22.96933 37.281 11.958 36.46133 57.80667 58.21167 19.95933 48.198 31.779 23.05967 22.16333 23.8 23.558 28.69233 45.90233 2964s sampleB_mean: 341.9077 165.372 131.954 21.142 143.015 59.789 312.258 16.70467 78.223 41.31433 42.12067 107.8423 84.293 77.04167 149.042 18.75567 33.19 72.11933 11.541 98.93967 40.62 173.185 176.0093 70.838 17.10933 28.83167 51.37267 107.4767 162.736 644.6073 40.211 21.17867 6.833333 17.62467 19.323 84.69133 60.698 15.272 60.63 230.7603 62.01667 231.01 361.5717 190.2367 147.5103 63.14733 24.36067 149.0183 11.974 91.85267 52.02367 47.04433 126.507 31.336 50.806 22.66633 52.632 35.05467 8.807333 20.43633 8.328333 21.66667 14.771 22.414 23.35133 126.2827 27.23467 43.86567 21.67633 25.96333 30.432 14.72967 1.413333 49.04333 113.391 61.038 34.63 35.93933 6.593 11.42567 43.19967 15.897 603.3247 15.84233 38.81867 11.08667 20.231 36.80733 7.705667 4.816667 13.23833 13.34567 21.97267 47.94933 11.73133 15.47833 24.79367 21.75133 84.23433 15.958 52.72333 3.929667 4.436 6.119333 5.855333 3.97 21.74967 6.474667 15.00967 126.723 14.15433 7.976 0 5.957333 7.353333 3.203 3.546 21.066 101.151 4.916 6.552 7.033333 15.06367 2.201333 6.709 7.766333 22.53 53.09067 21.36367 5.980333 34.28533 7.920333 1.620333 4.478333 5.375333 10.64267 14.63867 3.039667 8.861667 6.818 5.451 4.875667 3.831 3.745333 0 0 6.937333 1.439333 6.301667 8.477667 0 2.48 5.966667 3.384 3.374 14.62267 0.6883333 1.932 19.603 21.018 4.024 10.157 6.506333 1.628667 12.223 0 7.897667 41.35533 3.431333 9.145 7.386333 6.082333 10.15367 5.055333 2.116667 14.45 5.157 6.758333 10.28 1.101667 8.017333 4.993333 2.819 1.569 5.139 3.003333 8.006333 4.229333 1.765 8.693333 2.936333 2.849667 0.4836667 1.799 13.05267 25.41533 7.749 4.422333 1.63 2.893333 8.839667 6.500333 0.692 2.511 12.1 4.762667 2.462333 10.16333 5.261333 1.082 19.24567 5.417 4.954667 16.907 2.909667 5.873 4.677 0.8023333 3.485333 5.657333 0 0 1.766333 2.343667 8.528 2.217667 12.014 3.54 8.646 1.487333 4.158333 0.8846667 2.193667 4.627333 6.918667 2.344 2964s num discordant: 0 2964s validating: Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset 2964s File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test. 2964s sampleA_mean: 311.829 110.7323 658.8357 210.276 53.11833 77.55333 94.08633 1020.23 773.7893 112.322 825.1763 37.23367 28.62567 534.2237 407.2907 2661.226 117.2063 501.0717 220.5287 59.968 135.901 191.8153 105.9497 95.99433 138.353 124.4243 40.96933 65.965 55.75367 88.495 189.9813 24.33867 73.97767 62.58133 341.9023 62.68467 132.8633 36.84367 56.147 53.687 36.99433 81.05967 104.7537 83.305 48.72833 193.8337 53.33433 180.8457 50.429 42.797 47.89667 58.24233 57.313 49.103 21.54267 30.499 39.777 54.28 17.875 115.6623 12.42267 24.273 238.9387 4.98 336.3973 14.554 35.78433 25.096 23.53367 133.0233 30.00467 56.695 16.50567 12.544 19.86033 41.83033 199.8083 39.58367 17.029 41.80933 42.71533 3.969667 21.25867 17.60767 16.69733 23.71433 35.43333 57.13467 15.26033 68.49367 2.172 103.5143 342.208 24.38833 29.33233 14.56933 9.605 24.02367 63.41767 36.41067 31.04633 25.39133 20.959 45.89833 29.44033 10.63267 41.856 70.13033 6.926 24.772 6.981333 15.418 9.165333 21.14433 16.53733 8.362 6.042667 13.52433 32.75133 40.92067 16.22733 22.84267 75.059 56.92767 21.88967 21.31667 25.25367 28.28467 91.47333 7.960667 11.277 10.23233 15.914 31.61067 5.832 8.79 88.60033 15.28167 12.85033 17.12667 10.30967 7.374 40.359 49.53233 12.36 12.771 15.559 10.16833 23.029 65.86733 43.318 8.268 10.49233 5.097667 28.07033 11.38633 8.516333 20.27767 5.464 16.38067 18.746 21.686 3.122 31.838 3.966667 9.187667 12.023 5.342333 5.607667 35.59733 7.083 5.772333 7.825667 14.411 46.84667 21.776 21.765 54.65067 40.53433 7.526667 16.75833 18.06167 11.90333 6.314 32.918 16.17933 3.596 5.197667 5.960667 7.807333 2.752667 22.86533 12.81233 19.21233 15.31167 7.951 5.664333 22.029 25.534 8.48 12.13567 37.02633 10.73033 6.437333 8.47 22.12067 22.77967 2.539333 2.727 29.746 21.02533 8.809 14.33467 2.792667 3.51 14.356 11.03933 6.174667 3.046667 7.603667 23.46733 7.538 20.79733 12.918 27.34567 8.792667 6.934 6.306667 4.820333 9.925 11.28667 7.395 3.158 7.979667 17.25667 3.503 6.225667 0 7.501667 7.839333 5.134333 12.438 74.98367 7.113667 5.177333 3.531333 7.014667 5.639333 0.8883333 19.07367 3.201 14.50533 78.08667 3.788 13.76033 24.662 9.197667 7.025 6.052333 4.912333 5.777667 7.077333 10.31933 2.409667 8.232 7.901333 3.633333 1.506333 5.981333 3.867 8.591 7.560667 5.081 1.752333 8.047333 2.414667 0 10.41 5.407667 2.503 2.723333 9.876 2.105667 2.654667 3.773667 0 9.321667 2.518667 4.158 2.349 2.967333 7.296333 0 2.993667 3.311333 2.742667 6.318 2.888 1.734 5.546667 0 0 0.5686667 0 1.934333 23.97033 4.064667 4.931333 0.2506667 6.688 2.653333 8.351 3.471667 3.743 2.677333 7.922333 5.76 1.742333 3.082 10.97667 3.945333 6.958667 3.617 10.806 2.231667 0.4486667 19.41933 2.98 19.63133 2.767667 1.651333 0 3.012 2.625667 2964s sampleB_mean: 2830.628 1202.982 4216.251 2415.454 339.544 809.747 968.2863 5398.857 3709.705 2786.993 3756.434 461.5343 317.4807 4004.8 2355.907 13329.63 3506.467 2001.57 2047.901 266.1853 807.5603 1242.884 686.1263 878.6043 953.5553 513.784 501.3557 317.8843 222.0223 574.6353 926.6357 203.078 805.275 843.2847 1524.761 303.08 641.6557 208.1393 562.3953 256.6427 279.329 786.1327 468.317 401.8723 224.5063 731.863 371.2327 1012.972 573.2667 255.0223 265.6093 310.312 255.8583 290.862 255.2837 378.7327 157.5777 205.6727 116.6347 720.0863 166.8767 145.604 4759.337 1440.661 1576.856 148.789 178.71 166.0277 132.4173 1082.98 125.2547 387.0143 584.575 137.7833 121.5623 195.216 1109.48 320.243 286.777 158.383 263.0527 59.23867 168.2893 156.2033 151.719 120.8867 160.5167 232.1147 124.6713 585.796 58.96367 496.8353 1834.421 148.7563 161.1673 91.18133 109.3147 150.3003 477.213 148.6807 163.1987 156.0383 143.3147 178.2697 151.599 92.061 278.7393 311.44 41.78967 163.021 31.73 194.1133 177.154 213.8997 119.8297 51.73767 90.957 57.44367 219.6953 161.4237 194.3873 301.9357 332.2983 253.0167 109.0193 83.61967 174.6973 145.137 405.776 98.33933 110.8993 69.18967 117.851 160.1683 91.509 41.93 437.7257 143.0897 70.221 85.78933 53.655 143.872 188.56 195.2947 101.4477 118.1207 108.837 46.842 113.004 285.3807 193.3587 67.408 48.96533 87.65567 126.6913 64.15933 127.5543 138.9263 36.76567 109.6677 82.68433 141.442 91.739 263.5397 102.0507 54.097 96.804 24.80467 99.863 136.4563 64.25433 51.723 60.90233 179.874 216.4093 90.427 141.0183 230.7707 682.0817 71.949 76.82 91.49033 63.62167 71.81167 170.7463 93.09033 27.192 27.296 50.22033 29.00467 29.627 97.60633 96.94267 107.2877 130.4127 44.69833 47.31267 127.9993 94.78533 39.086 84.001 191.0543 55.476 56.05633 96.91167 112.8043 File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test. 2964s 918.9367 32.39667 36.6 120.0493 293.9087 49.09733 106.615 76.24933 37.96133 73.193 68.608 28.425 29.675 127.1577 169.1617 303.0437 125.7047 52.36933 174.409 44.98367 43.94933 41.517 68.67667 41.50267 84.252 28.775 30.93667 192.615 317.6723 20.82433 61.53933 174.965 31.52433 34.05967 40.13033 311.329 381.953 61.76067 30.54067 36.53367 27.23833 59.38567 19.95267 75.443 31.46 216.4057 356.891 24.244 76.899 176.0977 61.80233 58.12767 27.607 33.73067 251.767 28.714 48.14767 16.15667 42.92033 34.77567 19.99067 18.20933 24.384 30.03567 65.255 32.58033 54.54667 33.473 31.139 20.92033 19.80633 40.12533 21.00233 11.60833 31.73667 49.72933 28.15867 28.39433 24.241 18.23433 44.13267 26.27467 20.046 86.78467 12.202 33.75167 24.882 15.938 18.612 22.782 129.8027 23.60467 19.23067 19.744 6.507333 3.268 18.004 31.383 28.30833 106.4977 27.04033 20.212 19.36667 68.356 33.19833 54.89133 14.948 15.33767 72.35433 70.27367 28.421 38.715 31.89 73.018 20.05633 80.966 18.62033 68.52333 17.502 16.761 183.9787 16.92567 178.6527 17.09767 27.84133 14.14033 35.44867 19.71067 2964s num discordant: 0 2964s touch test_voom 2964s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR -m Trinity_trans.TMM.EXPR.matrix -s samples.txt --heatmap --sample_cor_matrix --log2 --save 2964s CMD: Rscript Trinity_trans.TMM.EXPR.matrix.R 2964s Loading required package: BiocGenerics 2965s 2965s Attaching package: ‘BiocGenerics’ 2965s 2965s The following objects are masked from ‘package:stats’: 2965s 2965s IQR, mad, sd, var, xtabs 2965s 2965s The following objects are masked from ‘package:base’: 2965s 2965s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 2965s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 2965s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 2965s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 2965s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 2965s tapply, union, unique, unsplit, which.max, which.min 2965s 2965s Welcome to Bioconductor 2965s 2965s Vignettes contain introductory material; view with 2965s 'browseVignettes()'. To cite Bioconductor, see 2965s 'citation("Biobase")', and for packages 'citation("pkgname")'. 2965s 2966s 2966s Attaching package: ‘fastcluster’ 2966s 2966s The following object is masked from ‘package:stats’: 2966s 2966s hclust 2966s 2966s [1] "Reading matrix file." 2966s for plotting:: min.raw: 0.647032826340685 max.raw: 1 2966s null device 2966s 1 2973s for plotting:: min.raw: 0 max.raw: 15.3986319455363 2973s null device 2973s 1 2986s touch test_PtR_heatmap 2986s ./validate_results.pl 2986s DESeq2_outdir/diffExpr.P0.001_C2.matrix, count: 1784 DE features OK. 2986s edgeR_outdir/diffExpr.P0.001_C2.matrix, count: 2063 DE features OK. 2986s make[2]: Leaving directory '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example' 2986s Running example in Spombe_example... 2986s voom_outdir/diffExpr.P0.001_C2.matrix, count: 1818 DE features OK. 2986s make[2]: Entering directory '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example' 2986s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_genes.counts.matrix --method edgeR -s samples.txt --dispersion 0.01 --output edgeR_genes 2986s Got 4 samples, and got: 5 data fields. 2986s Header: ds_rep1 hs_rep1 log_rep1 plat_rep1 2986s Next: TRINITY_DN5555_c0_g1 0.00 0.00 0.00 0.00 2986s 2986s $VAR1 = { 2986s 'log_rep1' => 3, 2986s 'ds_rep1' => 1, 2986s 'plat_rep1' => 4, 2986s 'hs_rep1' => 2 2986s }; 2986s $VAR1 = { 2986s 'plateau' => [ 2986s 'plat_rep1' 2986s ], 2986s 'log_growth' => [ 2986s 'log_rep1' 2986s ], 2986s 'heatshock' => [ 2986s 'hs_rep1' 2986s ], 2986s 'diauxic_shift' => [ 2986s 'ds_rep1' 2986s ] 2986s }; 2986s Contrasts to perform are: $VAR1 = [ 2986s [ 2986s 'diauxic_shift', 2986s 'heatshock' 2986s ], 2986s [ 2986s 'diauxic_shift', 2986s 'log_growth' 2986s ], 2986s [ 2986s 'diauxic_shift', 2986s 'plateau' 2986s ], 2986s [ 2986s 'heatshock', 2986s 'log_growth' 2986s ], 2986s [ 2986s 'heatshock', 2986s 'plateau' 2986s ], 2986s [ 2986s 'log_growth', 2986s 'plateau' 2986s ] 2986s ]; 2986s CMD: Rscript Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.diauxic_shift.vs.heatshock.EdgeR.Rscript 2986s Loading required package: edgeR 2986s Loading required package: limma 2987s null device 2987s 1 2987s CMD: Rscript Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.diauxic_shift.vs.log_growth.EdgeR.Rscript 2987s Loading required package: edgeR 2987s Loading required package: limma 2988s null device 2988s 1 2988s CMD: Rscript Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.diauxic_shift.vs.plateau.EdgeR.Rscript 2988s Loading required package: edgeR 2988s Loading required package: limma 2988s null device 2988s 1 2988s CMD: Rscript Trinity_genes.counts.matrix.heatshock_vs_log_growth.heatshock.vs.log_growth.EdgeR.Rscript 2988s Loading required package: edgeR 2988s Loading required package: limma 2989s null device 2989s 1 2989s CMD: Rscript Trinity_genes.counts.matrix.heatshock_vs_plateau.heatshock.vs.plateau.EdgeR.Rscript 2989s Loading required package: edgeR 2989s Loading required package: limma 2990s null device 2990s 1 2990s CMD: Rscript Trinity_genes.counts.matrix.log_growth_vs_plateau.log_growth.vs.plateau.EdgeR.Rscript 2990s Loading required package: edgeR 2990s Loading required package: limma 2990s null device 2990s 1 2990s cd edgeR_genes && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl -m ../Trinity_genes.TMM.EXPR.matrix \ 2990s -s ../samples.txt --examine_GO_enrichment --GO_annots ../Trinotate_report.xls.gene_ontology --gene_lengths ../Trinity_genes.lengths && \ 2990s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt 2990s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.heatshock-UP.subset --background Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.count_matrix 2991s Loading required package: BiasedUrn 2991s Loading required package: geneLenDataBase 3003s 3003s Loading required package: AnnotationDbi 3003s Loading required package: stats4 3003s Loading required package: BiocGenerics 3003s 3003s Attaching package: ‘BiocGenerics’ 3003s 3003s The following objects are masked from ‘package:stats’: 3003s 3003s IQR, mad, sd, var, xtabs 3003s 3003s The following objects are masked from ‘package:base’: 3003s 3003s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3003s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3003s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3003s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3003s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 3003s tapply, union, unique, unsplit, which.max, which.min 3003s 3003s Loading required package: Biobase 3003s Welcome to Bioconductor 3003s 3003s Vignettes contain introductory material; view with 3003s 'browseVignettes()'. To cite Bioconductor, see 3003s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3003s 3003s Loading required package: IRanges 3003s Loading required package: S4Vectors 3003s 3003s Attaching package: ‘S4Vectors’ 3003s 3003s The following object is masked from ‘package:geneLenDataBase’: 3003s 3003s unfactor 3003s 3003s The following object is masked from ‘package:utils’: 3003s 3003s findMatches 3003s 3003s The following objects are masked from ‘package:base’: 3003s 3003s expand.grid, I, unname 3003s 3004s Processing category: custom_list 3004s Using manually entered categories. 3005s Calculating the p-values... 3005s 'select()' returned 1:1 mapping between keys and columns 3006s 3006s 3006s Done. 3006s 3006s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.DE.subset --background Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.count_matrix 3006s Loading required package: BiasedUrn 3006s Loading required package: geneLenDataBase 3018s 3018s Loading required package: AnnotationDbi 3018s Loading required package: stats4 3018s Loading required package: BiocGenerics 3018s 3018s Attaching package: ‘BiocGenerics’ 3018s 3018s The following objects are masked from ‘package:stats’: 3018s 3018s IQR, mad, sd, var, xtabs 3018s 3018s The following objects are masked from ‘package:base’: 3018s 3018s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3018s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3018s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3018s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3018s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 3018s tapply, union, unique, unsplit, which.max, which.min 3018s 3018s Loading required package: Biobase 3018s Welcome to Bioconductor 3018s 3018s Vignettes contain introductory material; view with 3018s 'browseVignettes()'. To cite Bioconductor, see 3018s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3018s 3018s Loading required package: IRanges 3018s Loading required package: S4Vectors 3018s 3018s Attaching package: ‘S4Vectors’ 3018s 3018s The following object is masked from ‘package:geneLenDataBase’: 3018s 3018s unfactor 3018s 3018s The following object is masked from ‘package:utils’: 3018s 3018s findMatches 3018s 3018s The following objects are masked from ‘package:base’: 3018s 3018s expand.grid, I, unname 3018s 3019s Processing category: custom_list 3019s Using manually entered categories. 3020s Calculating the p-values... 3020s 'select()' returned 1:1 mapping between keys and columns 3020s 3020s 3020s Done. 3020s 3020s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset --background Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.count_matrix 3021s Loading required package: BiasedUrn 3021s Loading required package: geneLenDataBase 3032s 3032s Loading required package: AnnotationDbi 3032s Loading required package: stats4 3032s Loading required package: BiocGenerics 3032s 3032s Attaching package: ‘BiocGenerics’ 3032s 3032s The following objects are masked from ‘package:stats’: 3032s 3032s IQR, mad, sd, var, xtabs 3032s 3032s The following objects are masked from ‘package:base’: 3032s 3032s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3032s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3032s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3032s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3032s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 3032s tapply, union, unique, unsplit, which.max, which.min 3032s 3032s Loading required package: Biobase 3032s Welcome to Bioconductor 3032s 3032s Vignettes contain introductory material; view with 3032s 'browseVignettes()'. To cite Bioconductor, see 3032s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3032s 3032s Loading required package: IRanges 3032s Loading required package: S4Vectors 3032s 3032s Attaching package: ‘S4Vectors’ 3032s 3032s The following object is masked from ‘package:geneLenDataBase’: 3032s 3032s unfactor 3032s 3032s The following object is masked from ‘package:utils’: 3032s 3032s findMatches 3032s 3032s The following objects are masked from ‘package:base’: 3032s 3032s expand.grid, I, unname 3032s 3034s Processing category: custom_list 3034s Using manually entered categories. 3034s Calculating the p-values... 3035s 'select()' returned 1:1 mapping between keys and columns 3035s 3035s 3035s Done. 3035s 3035s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.DE.subset --background Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.count_matrix 3035s Loading required package: BiasedUrn 3035s Loading required package: geneLenDataBase 3047s 3047s Loading required package: AnnotationDbi 3047s Loading required package: stats4 3047s Loading required package: BiocGenerics 3047s 3047s Attaching package: ‘BiocGenerics’ 3047s 3047s The following objects are masked from ‘package:stats’: 3047s 3047s IQR, mad, sd, var, xtabs 3047s 3047s The following objects are masked from ‘package:base’: 3047s 3047s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3047s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3047s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3047s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3047s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 3047s tapply, union, unique, unsplit, which.max, which.min 3047s 3047s Loading required package: Biobase 3047s Welcome to Bioconductor 3047s 3047s Vignettes contain introductory material; view with 3047s 'browseVignettes()'. To cite Bioconductor, see 3047s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3047s 3047s Loading required package: IRanges 3047s Loading required package: S4Vectors 3047s 3047s Attaching package: ‘S4Vectors’ 3047s 3047s The following object is masked from ‘package:geneLenDataBase’: 3047s 3047s unfactor 3047s 3047s The following object is masked from ‘package:utils’: 3047s 3047s findMatches 3047s 3047s The following objects are masked from ‘package:base’: 3047s 3047s expand.grid, I, unname 3047s 3048s Processing category: custom_list 3048s Using manually entered categories. 3049s Calculating the p-values... 3049s 'select()' returned 1:1 mapping between keys and columns 3050s 3050s 3050s Done. 3050s 3050s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.heatshock-UP.subset --background Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.count_matrix 3050s Loading required package: BiasedUrn 3050s Loading required package: geneLenDataBase 3062s 3062s Loading required package: AnnotationDbi 3062s Loading required package: stats4 3062s Loading required package: BiocGenerics 3062s 3062s Attaching package: ‘BiocGenerics’ 3062s 3062s The following objects are masked from ‘package:stats’: 3062s 3062s IQR, mad, sd, var, xtabs 3062s 3062s The following objects are masked from ‘package:base’: 3062s 3062s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3062s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3062s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3062s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3062s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 3062s tapply, union, unique, unsplit, which.max, which.min 3062s 3062s Loading required package: Biobase 3062s Welcome to Bioconductor 3062s 3062s Vignettes contain introductory material; view with 3062s 'browseVignettes()'. To cite Bioconductor, see 3062s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3062s 3062s Loading required package: IRanges 3062s Loading required package: S4Vectors 3062s 3062s Attaching package: ‘S4Vectors’ 3062s 3062s The following object is masked from ‘package:geneLenDataBase’: 3062s 3062s unfactor 3062s 3062s The following object is masked from ‘package:utils’: 3062s 3062s findMatches 3062s 3062s The following objects are masked from ‘package:base’: 3062s 3062s expand.grid, I, unname 3062s 3067s Warning message: 3067s In pcls(G) : initial point very close to some inequality constraints 3067s Processing category: custom_list 3067s Using manually entered categories. 3067s Calculating the p-values... 3068s 'select()' returned 1:1 mapping between keys and columns 3069s 3069s 3069s Done. 3069s 3069s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset --background Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.count_matrix 3069s Loading required package: BiasedUrn 3069s Loading required package: geneLenDataBase 3082s 3082s Loading required package: AnnotationDbi 3082s Loading required package: stats4 3082s Loading required package: BiocGenerics 3082s 3082s Attaching package: ‘BiocGenerics’ 3082s 3082s The following objects are masked from ‘package:stats’: 3082s 3082s IQR, mad, sd, var, xtabs 3082s 3082s The following objects are masked from ‘package:base’: 3082s 3082s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3082s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3082s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3082s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3082s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 3082s tapply, union, unique, unsplit, which.max, which.min 3082s 3082s Loading required package: Biobase 3082s Welcome to Bioconductor 3082s 3082s Vignettes contain introductory material; view with 3082s 'browseVignettes()'. To cite Bioconductor, see 3082s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3082s 3082s Loading required package: IRanges 3082s Loading required package: S4Vectors 3082s 3082s Attaching package: ‘S4Vectors’ 3082s 3082s The following object is masked from ‘package:geneLenDataBase’: 3082s 3082s unfactor 3082s 3082s The following object is masked from ‘package:utils’: 3082s 3082s findMatches 3082s 3082s The following objects are masked from ‘package:base’: 3082s 3082s expand.grid, I, unname 3082s 3087s Processing category: custom_list 3087s Using manually entered categories. 3087s Calculating the p-values... 3088s 'select()' returned 1:1 mapping between keys and columns 3088s 3088s 3088s Done. 3088s 3088s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.DE.subset --background Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.count_matrix 3089s Loading required package: BiasedUrn 3089s Loading required package: geneLenDataBase 3101s 3101s Loading required package: AnnotationDbi 3101s Loading required package: stats4 3101s Loading required package: BiocGenerics 3101s 3101s Attaching package: ‘BiocGenerics’ 3101s 3101s The following objects are masked from ‘package:stats’: 3101s 3101s IQR, mad, sd, var, xtabs 3101s 3101s The following objects are masked from ‘package:base’: 3101s 3101s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3101s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3101s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3101s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3101s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 3101s tapply, union, unique, unsplit, which.max, which.min 3101s 3101s Loading required package: Biobase 3101s Welcome to Bioconductor 3101s 3101s Vignettes contain introductory material; view with 3101s 'browseVignettes()'. To cite Bioconductor, see 3101s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3101s 3101s Loading required package: IRanges 3101s Loading required package: S4Vectors 3101s 3101s Attaching package: ‘S4Vectors’ 3101s 3101s The following object is masked from ‘package:geneLenDataBase’: 3101s 3101s unfactor 3101s 3101s The following object is masked from ‘package:utils’: 3101s 3101s findMatches 3101s 3101s The following objects are masked from ‘package:base’: 3101s 3101s expand.grid, I, unname 3101s 3106s Warning message: 3106s In pcls(G) : initial point very close to some inequality constraints 3106s Processing category: custom_list 3106s Using manually entered categories. 3106s Calculating the p-values... 3106s 'select()' returned 1:1 mapping between keys and columns 3107s 3107s 3107s Done. 3107s 3107s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.heatshock-UP.subset --background Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.count_matrix 3108s Loading required package: BiasedUrn 3108s Loading required package: geneLenDataBase 3120s 3120s Loading required package: AnnotationDbi 3120s Loading required package: stats4 3120s Loading required package: BiocGenerics 3120s 3120s Attaching package: ‘BiocGenerics’ 3120s 3120s The following objects are masked from ‘package:stats’: 3120s 3120s IQR, mad, sd, var, xtabs 3120s 3120s The following objects are masked from ‘package:base’: 3120s 3120s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3120s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3120s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3120s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3120s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 3120s tapply, union, unique, unsplit, which.max, which.min 3120s 3120s Loading required package: Biobase 3120s Welcome to Bioconductor 3120s 3120s Vignettes contain introductory material; view with 3120s 'browseVignettes()'. To cite Bioconductor, see 3120s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3120s 3120s Loading required package: IRanges 3120s Loading required package: S4Vectors 3120s 3120s Attaching package: ‘S4Vectors’ 3120s 3120s The following object is masked from ‘package:geneLenDataBase’: 3120s 3120s unfactor 3120s 3120s The following object is masked from ‘package:utils’: 3120s 3120s findMatches 3120s 3120s The following objects are masked from ‘package:base’: 3120s 3120s expand.grid, I, unname 3120s 3122s Warning message: 3122s In newton(lsp = lsp, X = G$X, y = G$y, Eb = G$Eb, UrS = G$UrS, L = G$L, : 3122s Iteration limit reached without full convergence - check carefully 3122s Processing category: custom_list 3122s Using manually entered categories. 3122s Calculating the p-values... 3122s 'select()' returned 1:1 mapping between keys and columns 3123s 3123s 3123s Done. 3123s 3123s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.DE.subset --background Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.count_matrix 3123s Loading required package: BiasedUrn 3123s Loading required package: geneLenDataBase 3135s 3135s Loading required package: AnnotationDbi 3135s Loading required package: stats4 3135s Loading required package: BiocGenerics 3135s 3135s Attaching package: ‘BiocGenerics’ 3135s 3135s The following objects are masked from ‘package:stats’: 3135s 3135s IQR, mad, sd, var, xtabs 3135s 3135s The following objects are masked from ‘package:base’: 3135s 3135s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3135s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3135s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3135s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3135s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 3135s tapply, union, unique, unsplit, which.max, which.min 3135s 3135s Loading required package: Biobase 3135s Welcome to Bioconductor 3135s 3135s Vignettes contain introductory material; view with 3135s 'browseVignettes()'. To cite Bioconductor, see 3135s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3135s 3135s Loading required package: IRanges 3135s Loading required package: S4Vectors 3135s 3135s Attaching package: ‘S4Vectors’ 3135s 3135s The following object is masked from ‘package:geneLenDataBase’: 3135s 3135s unfactor 3135s 3135s The following object is masked from ‘package:utils’: 3135s 3135s findMatches 3135s 3135s The following objects are masked from ‘package:base’: 3135s 3135s expand.grid, I, unname 3135s 3138s Warning message: 3138s In newton(lsp = lsp, X = G$X, y = G$y, Eb = G$Eb, UrS = G$UrS, L = G$L, : 3138s Iteration limit reached without full convergence - check carefully 3138s Processing category: custom_list 3138s Using manually entered categories. 3138s Calculating the p-values... 3138s 'select()' returned 1:1 mapping between keys and columns 3139s 3139s 3139s Done. 3139s 3139s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.log_growth-UP.subset --background Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.count_matrix 3139s Loading required package: BiasedUrn 3139s Loading required package: geneLenDataBase 3151s 3151s Loading required package: AnnotationDbi 3151s Loading required package: stats4 3151s Loading required package: BiocGenerics 3151s 3151s Attaching package: ‘BiocGenerics’ 3151s 3151s The following objects are masked from ‘package:stats’: 3151s 3151s IQR, mad, sd, var, xtabs 3151s 3151s The following objects are masked from ‘package:base’: 3151s 3151s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3151s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3151s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3151s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3151s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 3151s tapply, union, unique, unsplit, which.max, which.min 3151s 3151s Loading required package: Biobase 3151s Welcome to Bioconductor 3151s 3151s Vignettes contain introductory material; view with 3151s 'browseVignettes()'. To cite Bioconductor, see 3151s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3151s 3151s Loading required package: IRanges 3151s Loading required package: S4Vectors 3151s 3151s Attaching package: ‘S4Vectors’ 3151s 3151s The following object is masked from ‘package:geneLenDataBase’: 3151s 3151s unfactor 3151s 3151s The following object is masked from ‘package:utils’: 3151s 3151s findMatches 3151s 3151s The following objects are masked from ‘package:base’: 3151s 3151s expand.grid, I, unname 3151s 3153s Processing category: custom_list 3153s Using manually entered categories. 3153s Calculating the p-values... 3153s 'select()' returned 1:1 mapping between keys and columns 3154s 3154s 3154s Done. 3154s 3154s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.DE.subset --background Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.count_matrix 3154s Loading required package: BiasedUrn 3154s Loading required package: geneLenDataBase 3166s 3166s Loading required package: AnnotationDbi 3166s Loading required package: stats4 3166s Loading required package: BiocGenerics 3166s 3166s Attaching package: ‘BiocGenerics’ 3166s 3166s The following objects are masked from ‘package:stats’: 3166s 3166s IQR, mad, sd, var, xtabs 3166s 3166s The following objects are masked from ‘package:base’: 3166s 3166s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3166s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3166s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3166s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3166s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 3166s tapply, union, unique, unsplit, which.max, which.min 3166s 3166s Loading required package: Biobase 3166s Welcome to Bioconductor 3166s 3166s Vignettes contain introductory material; view with 3166s 'browseVignettes()'. To cite Bioconductor, see 3166s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3166s 3166s Loading required package: IRanges 3166s Loading required package: S4Vectors 3166s 3166s Attaching package: ‘S4Vectors’ 3166s 3166s The following object is masked from ‘package:geneLenDataBase’: 3166s 3166s unfactor 3166s 3166s The following object is masked from ‘package:utils’: 3166s 3166s findMatches 3166s 3166s The following objects are masked from ‘package:base’: 3166s 3166s expand.grid, I, unname 3166s 3169s Processing category: custom_list 3169s Using manually entered categories. 3169s Calculating the p-values... 3169s 'select()' returned 1:1 mapping between keys and columns 3169s 3169s 3169s Done. 3169s 3169s 3169s 3169s ** Found 25 features as differentially expressed. 3169s 3169s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR -m diffExpr.P0.001_C2.matrix --log2 --heatmap --min_colSums 0 --min_rowSums 0 --gene_dist euclidean --sample_dist euclidean --sample_cor_matrix --center_rows --save -s ../samples.txt 3169s CMD: Rscript diffExpr.P0.001_C2.matrix.R 3169s Loading required package: BiocGenerics 3170s 3170s Attaching package: ‘BiocGenerics’ 3170s 3170s The following objects are masked from ‘package:stats’: 3170s 3170s IQR, mad, sd, var, xtabs 3170s 3170s The following objects are masked from ‘package:base’: 3170s 3170s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 3170s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 3170s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 3170s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 3170s Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, 3170s tapply, union, unique, unsplit, which.max, which.min 3170s 3170s Welcome to Bioconductor 3170s 3170s Vignettes contain introductory material; view with 3170s 'browseVignettes()'. To cite Bioconductor, see 3170s 'citation("Biobase")', and for packages 'citation("pkgname")'. 3170s 3171s 3171s Attaching package: ‘fastcluster’ 3171s 3171s [1] "Reading matrix file." 3171s The following object is masked from ‘package:stats’: 3171s 3171s hclust 3171s 3171s for plotting:: min.raw: -0.790731955608766 max.raw: 1 3171s null device 3171s 1 3171s for plotting:: min.raw: -9.76652141391246 max.raw: 9.76652141391246 3171s null device 3171s 1 3172s validating: Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset 3172s validating: Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.heatshock-UP.subset 3172s sampleA_mean: 351.239 3172s sampleB_mean: 10243.92 3172s num discordant: 0 3172s validating: Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset 3172s no DE entries reported here. 3172s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset) passes test. 3172s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.heatshock-UP.subset) passes test. 3172s no DE entries reported here. 3172s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset) passes test. 3172s no DE entries reported here. 3172s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset) passes test. 3172s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset) passes test. 3172s no DE entries reported here. 3172s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset) passes test. 3172s validating: Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset 3172s validating: Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset 3172s sampleA_mean: 24474.99 3172s sampleB_mean: 655.981 3172s num discordant: 0 3172s validating: Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset 3172s validating: Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.heatshock-UP.subset 3172s sampleA_mean: 55553.11 9045.287 7701.044 14784.77 3821.721 6809.755 5432.001 5230.464 5420.566 11308.68 3399.73 7103.994 7754.294 8095.973 3638.996 4829.911 6463.777 5768.825 4014.476 4247.003 3172s sampleB_mean: 296.91 747.095 126.015 319.249 55.433 375.614 535.795 440.221 397.102 1596.57 221.609 176.425 409.173 810.001 115.22 165.063 1510.474 763.865 412.434 854.558 3172s num discordant: 0 3172s validating: Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset 3172s sampleA_mean: 2036.649 135.207 3172s sampleB_mean: 11080.21 1620.935 3172s num discordant: 0 3172s validating: Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.heatshock-UP.subset 3172s sampleA_mean: 7754.294 3172s sampleB_mean: 252.38 3172s num discordant: 0 3172s validating: Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset 3172s File: (Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.heatshock-UP.subset) passes test. 3172s File: (Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset) passes test. 3172s File: (Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.heatshock-UP.subset) passes test. 3172s validating: Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.log_growth-UP.subset 3172s sampleA_mean: 9466.084 3172s sampleB_mean: 470.915 3172s num discordant: 0 3172s validating: Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset 3172s no DE entries reported here. 3172s File: (Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset) passes test. 3172s File: (Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.log_growth-UP.subset) passes test. 3172s no DE entries reported here. 3172s File: (Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset) passes test. 3172s ./validate_results.pl 3172s edgeR_genes/diffExpr.P0.001_C2.matrix, count: 26 DE features OK. 3172s edgeR_genes/Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.DE.subset.GOseq.enriched, count: 112 DE features OK. 3172s edgeR_genes/Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset.GOseq.enriched, count: 46 DE features OK. 3172s touch test 3172s make[2]: Leaving directory '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example' 3172s make[1]: Leaving directory '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis' 3172s Running example in test_align_and_estimate_abundance... 3172s make[1]: Entering directory '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance' 3172s Running example in PAIRED_END_ABUNDANCE_ESTIMATION... 3172s make[2]: Entering directory '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION' 3172s ../align_and_estimate_tester.pl RSEM "samples.txt" "../../test_DATA/Trinity.fasta" 3172s CMD: ln -sf ../../test_DATA/Trinity.fasta . 3172s CMD: /usr/lib/trinityrnaseq/util/align_and_estimate_abundance.pl --transcripts Trinity.fasta --prep_reference --left /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.left.fq.gz --right /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.right.fq.gz --SS_lib_type RF --seqType fq --trinity_mode --est_method RSEM --output_dir RSEM-heatshock --aln_method bowtie2 --coordsort_bam 3172s CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta > /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.gene_trans_map 3172s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.started 3172s CMD: bowtie2-build /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2 3172s Settings: 3172s Output files: "/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.*.bt2" 3172s Line rate: 6 (line is 64 bytes) 3172s Lines per side: 1 (side is 64 bytes) 3172s Offset rate: 4 (one in 16) 3172s FTable chars: 10 3172s Strings: unpacked 3172s Max bucket size: default 3172s Max bucket size, sqrt multiplier: default 3172s Max bucket size, len divisor: 4 3172s Difference-cover sample period: 1024 3172s Endianness: little 3172s Actual local endianness: little 3172s Sanity checking: disabled 3172s Assertions: disabled 3172s Random seed: 0 3172s Sizeofs: void*:8, int:4, long:8, size_t:8 3172s Input files DNA, FASTA: 3172s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta 3172s Reading reference sizes 3172s Building a SMALL index 3172s Time reading reference sizes: 00:00:00 3172s Calculating joined length 3172s Writing header 3172s Reserving space for joined string 3172s Joining reference sequences 3172s Time to join reference sequences: 00:00:00 3172s bmax according to bmaxDivN setting: 54360 3172s Using parameters --bmax 40770 --dcv 1024 3172s Doing ahead-of-time memory usage test 3172s Passed! Constructing with these parameters: --bmax 40770 --dcv 1024 3172s Constructing suffix-array element generator 3172s Building DifferenceCoverSample 3172s Building sPrime 3172s Building sPrimeOrder 3172s V-Sorting samples 3172s V-Sorting samples time: 00:00:00 3172s Allocating rank array 3172s Ranking v-sort output 3172s Ranking v-sort output time: 00:00:00 3172s Invoking Larsson-Sadakane on ranks 3172s Invoking Larsson-Sadakane on ranks time: 00:00:00 3172s Sanity-checking and returning 3172s Building samples 3172s Reserving space for 12 sample suffixes 3172s Generating random suffixes 3172s QSorting 12 sample offsets, eliminating duplicates 3172s QSorting sample offsets, eliminating duplicates time: 00:00:00 3172s Multikey QSorting 12 samples 3172s (Using difference cover) 3172s Multikey QSorting samples time: 00:00:00 3172s Calculating bucket sizes 3172s Splitting and merging 3172s Splitting and merging time: 00:00:00 3172s Split 2, merged 6; iterating... 3172s Splitting and merging 3172s Splitting and merging time: 00:00:00 3172s Split 1, merged 2; iterating... 3172s Splitting and merging 3172s Splitting and merging time: 00:00:00 3172s Split 1, merged 0; iterating... 3172s Splitting and merging 3172s Splitting and merging time: 00:00:00 3172s Avg bucket size: 27179.5 (target: 40769) 3172s Converting suffix-array elements to index image 3172s Allocating ftab, absorbFtab 3172s Entering Ebwt loop 3172s Getting block 1 of 8 3172s Reserving size (40770) for bucket 1 3172s Calculating Z arrays for bucket 1 3172s Entering block accumulator loop for bucket 1: 3172s bucket 1: 10% 3172s bucket 1: 20% 3172s bucket 1: 30% 3172s bucket 1: 40% 3172s bucket 1: 50% 3172s bucket 1: 60% 3172s bucket 1: 70% 3172s bucket 1: 80% 3172s bucket 1: 90% 3172s bucket 1: 100% 3172s Sorting block of length 34231 for bucket 1 3172s (Using difference cover) 3172s Sorting block time: 00:00:00 3172s Returning block of 34232 for bucket 1 3172s Getting block 2 of 8 3172s Reserving size (40770) for bucket 2 3172s Calculating Z arrays for bucket 2 3172s Entering block accumulator loop for bucket 2: 3172s bucket 2: 10% 3172s bucket 2: 20% 3172s bucket 2: 30% 3172s bucket 2: 40% 3172s bucket 2: 50% 3172s bucket 2: 60% 3172s bucket 2: 70% 3172s bucket 2: 80% 3172s bucket 2: 90% 3172s bucket 2: 100% 3172s Sorting block of length 39793 for bucket 2 3172s (Using difference cover) 3172s Sorting block time: 00:00:00 3172s Returning block of 39794 for bucket 2 3172s Getting block 3 of 8 3172s Reserving size (40770) for bucket 3 3172s Calculating Z arrays for bucket 3 3172s Entering block accumulator loop for bucket 3: 3172s bucket 3: 10% 3172s bucket 3: 20% 3172s bucket 3: 30% 3172s bucket 3: 40% 3172s bucket 3: 50% 3172s bucket 3: 60% 3172s bucket 3: 70% 3172s bucket 3: 80% 3172s bucket 3: 90% 3172s bucket 3: 100% 3172s Sorting block of length 9793 for bucket 3 3172s (Using difference cover) 3172s Sorting block time: 00:00:00 3172s Returning block of 9794 for bucket 3 3172s Getting block 4 of 8 3172s Reserving size (40770) for bucket 4 3172s Calculating Z arrays for bucket 4 3172s Entering block accumulator loop for bucket 4: 3172s bucket 4: 10% 3172s bucket 4: 20% 3172s bucket 4: 30% 3172s bucket 4: 40% 3172s bucket 4: 50% 3172s bucket 4: 60% 3172s bucket 4: 70% 3172s bucket 4: 80% 3172s bucket 4: 90% 3172s bucket 4: 100% 3172s Sorting block of length 31901 for bucket 4 3172s (Using difference cover) 3172s Sorting block time: 00:00:00 3172s Returning block of 31902 for bucket 4 3172s Getting block 5 of 8 3172s Reserving size (40770) for bucket 5 3172s Calculating Z arrays for bucket 5 3172s Entering block accumulator loop for bucket 5: 3172s bucket 5: 10% 3172s bucket 5: 20% 3172s bucket 5: 30% 3172s bucket 5: 40% 3172s bucket 5: 50% 3172s bucket 5: 60% 3172s bucket 5: 70% 3172s bucket 5: 80% 3172s bucket 5: 90% 3172s bucket 5: 100% 3172s Sorting block of length 10600 for bucket 5 3172s (Using difference cover) 3172s Sorting block time: 00:00:00 3172s Returning block of 10601 for bucket 5 3172s Getting block 6 of 8 3172s Reserving size (40770) for bucket 6 3172s Calculating Z arrays for bucket 6 3172s Entering block accumulator loop for bucket 6: 3172s bucket 6: 10% 3172s bucket 6: 20% 3172s bucket 6: 30% 3172s bucket 6: 40% 3172s bucket 6: 50% 3172s bucket 6: 60% 3172s bucket 6: 70% 3172s bucket 6: 80% 3172s bucket 6: 90% 3172s bucket 6: 100% 3172s Sorting block of length 40652 for bucket 6 3172s (Using difference cover) 3172s Sorting block time: 00:00:00 3172s Returning block of 40653 for bucket 6 3172s Getting block 7 of 8 3172s Reserving size (40770) for bucket 7 3172s Calculating Z arrays for bucket 7 3172s Entering block accumulator loop for bucket 7: 3172s bucket 7: 10% 3172s bucket 7: 20% 3172s bucket 7: 30% 3172s bucket 7: 40% 3172s bucket 7: 50% 3172s bucket 7: 60% 3172s bucket 7: 70% 3172s bucket 7: 80% 3172s bucket 7: 90% 3172s bucket 7: 100% 3172s Sorting block of length 18337 for bucket 7 3172s (Using difference cover) 3172s Sorting block time: 00:00:00 3172s Returning block of 18338 for bucket 7 3172s Getting block 8 of 8 3172s Reserving size (40770) for bucket 8 3172s Calculating Z arrays for bucket 8 3172s Entering block accumulator loop for bucket 8: 3172s bucket 8: 10% 3172s bucket 8: 20% 3172s bucket 8: 30% 3172s bucket 8: 40% 3172s bucket 8: 50% 3172s bucket 8: 60% 3172s bucket 8: 70% 3172s bucket 8: 80% 3172s bucket 8: 90% 3172s bucket 8: 100% 3172s Sorting block of length 32129 for bucket 8 3172s (Using difference cover) 3172s Sorting block time: 00:00:00 3172s Returning block of 32130 for bucket 8 3172s Exited Ebwt loop 3172s fchr[A]: 0 3172s fchr[C]: 59864 3172s fchr[G]: 108205 3172s fchr[T]: 157829 3172s fchr[$]: 217443 3172s Exiting Ebwt::buildToDisk() 3172s Returning from initFromVector 3172s Wrote 4313663 bytes to primary EBWT file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.1.bt2.tmp 3172s Wrote 54368 bytes to secondary EBWT file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.2.bt2.tmp 3172s Re-opening _in1 and _in2 as input streams 3172s Returning from Ebwt constructor 3172s Headers: 3172s len: 217443 3172s bwtLen: 217444 3172s sz: 54361 3172s bwtSz: 54361 3172s lineRate: 6 3172s offRate: 4 3172s offMask: 0xfffffff0 3172s ftabChars: 10 3172s eftabLen: 20 3172s eftabSz: 80 3172s ftabLen: 1048577 3172s ftabSz: 4194308 3172s offsLen: 13591 3172s offsSz: 54364 3172s lineSz: 64 3172s sideSz: 64 3172s sideBwtSz: 48 3172s sideBwtLen: 192 3172s numSides: 1133 3172s numLines: 1133 3172s ebwtTotLen: 72512 3172s ebwtTotSz: 72512 3172s color: 0 3172s reverse: 0 3172s Total time for call to driver() for forward index: 00:00:00 3172s Reading reference sizes 3172s Time reading reference sizes: 00:00:00 3172s Calculating joined length 3172s Writing header 3172s Reserving space for joined string 3172s Joining reference sequences 3172s Time to join reference sequences: 00:00:00 3172s Time to reverse reference sequence: 00:00:00 3172s bmax according to bmaxDivN setting: 54360 3172s Using parameters --bmax 40770 --dcv 1024 3172s Doing ahead-of-time memory usage test 3172s Passed! Constructing with these parameters: --bmax 40770 --dcv 1024 3172s Constructing suffix-array element generator 3172s Building DifferenceCoverSample 3172s Building sPrime 3172s Building sPrimeOrder 3172s V-Sorting samples 3172s V-Sorting samples time: 00:00:00 3172s Allocating rank array 3172s Ranking v-sort output 3172s Ranking v-sort output time: 00:00:00 3172s Invoking Larsson-Sadakane on ranks 3172s Invoking Larsson-Sadakane on ranks time: 00:00:00 3172s Sanity-checking and returning 3172s Building samples 3172s Reserving space for 12 sample suffixes 3172s Generating random suffixes 3172s QSorting 12 sample offsets, eliminating duplicates 3172s QSorting sample offsets, eliminating duplicates time: 00:00:00 3172s Multikey QSorting 12 samples 3172s (Using difference cover) 3172s Multikey QSorting samples time: 00:00:00 3172s Calculating bucket sizes 3172s Splitting and merging 3172s Splitting and merging time: 00:00:00 3172s Split 1, merged 6; iterating... 3172s Splitting and merging 3172s Splitting and merging time: 00:00:00 3172s Avg bucket size: 31062.4 (target: 40769) 3172s Converting suffix-array elements to index image 3172s Allocating ftab, absorbFtab 3172s Entering Ebwt loop 3172s Getting block 1 of 7 3172s Reserving size (40770) for bucket 1 3172s Calculating Z arrays for bucket 1 3172s Entering block accumulator loop for bucket 1: 3172s bucket 1: 10% 3172s bucket 1: 20% 3172s bucket 1: 30% 3172s bucket 1: 40% 3172s bucket 1: 50% 3172s bucket 1: 60% 3172s bucket 1: 70% 3172s bucket 1: 80% 3172s bucket 1: 90% 3172s bucket 1: 100% 3172s Sorting block of length 37058 for bucket 1 3172s (Using difference cover) 3172s Sorting block time: 00:00:00 3172s Returning block of 37059 for bucket 1 3172s Getting block 2 of 7 3172s Reserving size (40770) for bucket 2 3172s Calculating Z arrays for bucket 2 3172s Entering block accumulator loop for bucket 2: 3172s bucket 2: 10% 3172s bucket 2: 20% 3172s bucket 2: 30% 3172s bucket 2: 40% 3172s bucket 2: 50% 3172s bucket 2: 60% 3172s bucket 2: 70% 3172s bucket 2: 80% 3172s bucket 2: 90% 3172s bucket 2: 100% 3172s Sorting block of length 17846 for bucket 2 3172s (Using difference cover) 3172s Sorting block time: 00:00:00 3172s Returning block of 17847 for bucket 2 3172s Getting block 3 of 7 3172s Reserving size (40770) for bucket 3 3172s Calculating Z arrays for bucket 3 3172s Entering block accumulator loop for bucket 3: 3172s bucket 3: 10% 3172s bucket 3: 20% 3172s bucket 3: 30% 3172s bucket 3: 40% 3172s bucket 3: 50% 3172s bucket 3: 60% 3172s bucket 3: 70% 3172s bucket 3: 80% 3172s bucket 3: 90% 3172s bucket 3: 100% 3172s Sorting block of length 39327 for bucket 3 3172s (Using difference cover) 3172s Sorting block time: 00:00:00 3172s Returning block of 39328 for bucket 3 3172s Getting block 4 of 7 3172s Reserving size (40770) for bucket 4 3172s Calculating Z arrays for bucket 4 3172s Entering block accumulator loop for bucket 4: 3172s bucket 4: 10% 3172s bucket 4: 20% 3172s bucket 4: 30% 3172s bucket 4: 40% 3172s bucket 4: 50% 3172s bucket 4: 60% 3172s bucket 4: 70% 3172s bucket 4: 80% 3172s bucket 4: 90% 3172s bucket 4: 100% 3172s Sorting block of length 34139 for bucket 4 3172s (Using difference cover) 3172s Sorting block time: 00:00:00 3172s Returning block of 34140 for bucket 4 3172s Getting block 5 of 7 3172s Reserving size (40770) for bucket 5 3172s Calculating Z arrays for bucket 5 3172s Entering block accumulator loop for bucket 5: 3172s bucket 5: 10% 3172s bucket 5: 20% 3172s bucket 5: 30% 3172s bucket 5: 40% 3172s bucket 5: 50% 3172s bucket 5: 60% 3172s bucket 5: 70% 3172s bucket 5: 80% 3172s bucket 5: 90% 3172s bucket 5: 100% 3172s Sorting block of length 31038 for bucket 5 3172s (Using difference cover) 3172s Sorting block time: 00:00:00 3172s Returning block of 31039 for bucket 5 3172s Getting block 6 of 7 3172s Reserving size (40770) for bucket 6 3172s Calculating Z arrays for bucket 6 3172s Entering block accumulator loop for bucket 6: 3172s bucket 6: 10% 3172s bucket 6: 20% 3172s bucket 6: 30% 3172s bucket 6: 40% 3172s bucket 6: 50% 3172s bucket 6: 60% 3172s bucket 6: 70% 3172s bucket 6: 80% 3172s bucket 6: 90% 3172s bucket 6: 100% 3172s Sorting block of length 21215 for bucket 6 3172s (Using difference cover) 3172s Sorting block time: 00:00:00 3172s Returning block of 21216 for bucket 6 3172s Getting block 7 of 7 3172s Reserving size (40770) for bucket 7 3172s Calculating Z arrays for bucket 7 3172s Entering block accumulator loop for bucket 7: 3172s bucket 7: 10% 3172s bucket 7: 20% 3172s bucket 7: 30% 3172s bucket 7: 40% 3172s bucket 7: 50% 3172s bucket 7: 60% 3172s bucket 7: 70% 3172s bucket 7: 80% 3172s bucket 7: 90% 3172s bucket 7: 100% 3172s Sorting block of length 36814 for bucket 7 3172s (Using difference cover) 3172s Sorting block time: 00:00:00 3172s Returning block of 36815 for bucket 7 3172s Exited Ebwt loop 3172s fchr[A]: 0 3172s fchr[C]: 59864 3172s fchr[G]: 108205 3172s fchr[T]: 157829 3172s fchr[$]: 217443 3172s Exiting Ebwt::buildToDisk() 3172s Returning from initFromVector 3172s Wrote 4313663 bytes to primary EBWT file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.1.bt2.tmp 3172s Wrote 54368 bytes to secondary EBWT file: /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.2.bt2.tmp 3172s Re-opening _in1 and _in2 as input streams 3172s Returning from Ebwt constructor 3172s Headers: 3172s len: 217443 3172s bwtLen: 217444 3172s sz: 54361 3172s bwtSz: 54361 3172s lineRate: 6 3172s offRate: 4 3172s offMask: 0xfffffff0 3172s ftabChars: 10 3172s eftabLen: 20 3172s eftabSz: 80 3172s ftabLen: 1048577 3172s ftabSz: 4194308 3172s offsLen: 13591 3172s offsSz: 54364 3172s lineSz: 64 3172s sideSz: 64 3172s sideBwtSz: 48 3172s sideBwtLen: 192 3172s numSides: 1133 3172s numLines: 1133 3172s ebwtTotLen: 72512 3172s ebwtTotSz: 72512 3172s color: 0 3172s reverse: 1 3172s Total time for backward call to driver() for mirror index: 00:00:00 3172s Renaming /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.3.bt2.tmp to /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.3.bt2 3172s Renaming /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.4.bt2.tmp to /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.4.bt2 3172s Renaming /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.1.bt2.tmp to /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.1.bt2 3172s Renaming /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.2.bt2.tmp to /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.2.bt2 3172s Renaming /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.1.bt2.tmp to /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.1.bt2 3172s Renaming /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.2.bt2.tmp to /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.2.bt2 3172s CMD: touch /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.rsem.prepped.started 3172s CMD: rsem-prepare-reference --transcript-to-gene-map /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.gene_trans_map /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM 3172s rsem-synthesis-reference-transcripts /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM 0 1 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.gene_trans_map /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta 3173s Transcript Information File is generated! 3173s Group File is generated! 3173s Extracted Sequences File is generated! 3173s 3173s rsem-preref /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.transcripts.fa 1 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM 3173s Refs.makeRefs finished! 3173s Refs.saveRefs finished! 3173s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.idx.fa is generated! 3173s /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.n2g.idx.fa is generated! 3173s 3173s $VAR1 = [ 3173s { 3173s 'right' => '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.right.fq.gz', 3173s 'output_dir' => 'RSEM-heatshock', 3173s 'left' => '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.left.fq.gz' 3173s } 3173s ]; 3173s CMD: set -o pipefail && bowtie2 --no-mixed --no-discordant --gbar 1000 --end-to-end -k 200 -q -X 800 -x /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2 -1 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.left.fq.gz -2 /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.right.fq.gz -p 4 | samtools view -@ 4 -F 4 -S -b | samtools sort -@ 4 -n -o bowtie2.bam 3173s 10000 reads; of these: 3173s 10000 (100.00%) were paired; of these: 3173s 7088 (70.88%) aligned concordantly 0 times 3173s 1764 (17.64%) aligned concordantly exactly 1 time 3173s 1148 (11.48%) aligned concordantly >1 times 3173s 29.12% overall alignment rate 3173s [bam_sort_core] merging from 0 files and 4 in-memory blocks... 3173s CMD: touch bowtie2.bam.ok 3173s CMD: convert-sam-for-rsem -p 4 bowtie2.bam bowtie2.bam.for_rsem 3174s samtools sort -n -@ 4 -m 1G -o bowtie2.bam.for_rsem.tmp.bam bowtie2.bam 3174s samtools sort: couldn't allocate memory for bam_mem 3174s "samtools sort -n -@ 4 -m 1G -o bowtie2.bam.for_rsem.tmp.bam bowtie2.bam" failed! Plase check if you provide correct parameters/options for the pipeline! 3174s Error, cmd: convert-sam-for-rsem -p 4 bowtie2.bam bowtie2.bam.for_rsem died with ret: 65280 at /usr/lib/trinityrnaseq/util/align_and_estimate_abundance.pl line 728. 3174s Error, cmd: 3174s /usr/lib/trinityrnaseq/util/align_and_estimate_abundance.pl --transcripts Trinity.fasta --prep_reference --left /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.left.fq.gz --right /tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.right.fq.gz --SS_lib_type RF --seqType fq --trinity_mode --est_method RSEM --output_dir RSEM-heatshock --aln_method bowtie2 --coordsort_bam 3174s died with ret (512) at /usr/lib/trinityrnaseq/PerlLib/Process_cmd.pm line 19. 3174s Process_cmd::process_cmd("/usr/lib/trinityrnaseq/util/align_and_estimate_abundance.pl -"...) called at ../align_and_estimate_tester.pl line 98 3174s make[2]: Leaving directory '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION' 3174s make[2]: *** [Makefile:25: test_RSEM] Error 2 3174s make[1]: Leaving directory '/tmp/autopkgtest.zV67tP/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance' 3174s make[1]: *** [Makefile:8: test] Error 2 3174s make: *** [Makefile:18: test] Error 2 3174s autopkgtest [18:29:50]: test run-tests: -----------------------] 3174s autopkgtest [18:29:50]: test run-tests: - - - - - - - - - - results - - - - - - - - - - 3174s run-tests FAIL non-zero exit status 2 3176s autopkgtest [18:29:52]: @@@@@@@@@@@@@@@@@@@@ summary 3176s run-tests FAIL non-zero exit status 2 3187s nova [W] Skipping flock for amd64 3187s Creating nova instance adt-plucky-amd64-trinityrnaseq-20241102-170137-juju-7f2275-prod-proposed-migration-environment-2-4ebdd19d-d423-489e-865f-47c430b49833 from image adt/ubuntu-plucky-amd64-server-20241102.img (UUID 640916e2-9412-4fa2-8155-f822a4055b51)...