0s autopkgtest [13:57:46]: starting date and time: 2024-11-04 13:57:46+0000
  0s autopkgtest [13:57:46]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [13:57:46]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.88bjqok7/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:htslib --apt-upgrade trinityrnaseq --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=htslib/1.20+ds-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-60.secgroup --name adt-plucky-amd64-trinityrnaseq-20241104-124444-juju-7f2275-prod-proposed-migration-environment-2-8ddd7891-3aa5-4000-b615-0d9b2a85ced4 --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/
621s autopkgtest [14:08:07]: testbed dpkg architecture: amd64
621s autopkgtest [14:08:07]: testbed apt version: 2.9.8
621s autopkgtest [14:08:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup
621s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
621s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2268 kB]
621s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [31.2 kB]
621s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB]
621s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
621s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [165 kB]
621s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [238 kB]
621s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB]
621s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [833 kB]
621s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [1715 kB]
621s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [58.6 kB]
621s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [18.1 kB]
622s Fetched 5618 kB in 1s (9855 kB/s)
622s Reading package lists...
623s Reading package lists...
624s Building dependency tree...
624s Reading state information...
624s Calculating upgrade...
625s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
625s Reading package lists...
625s Building dependency tree...
625s Reading state information...
625s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
625s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
625s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
625s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
625s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
627s Reading package lists...
627s Reading package lists...
627s Building dependency tree...
627s Reading state information...
627s Calculating upgrade...
628s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
628s Reading package lists...
628s Building dependency tree...
628s Reading state information...
628s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
629s autopkgtest [14:08:15]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024
629s autopkgtest [14:08:15]: @@@@@@@@@@@@@@@@@@@@ apt-source trinityrnaseq
633s Get:1 http://ftpmaster.internal/ubuntu plucky/universe trinityrnaseq 2.15.1+dfsg-5build1 (dsc) [2629 B]
633s Get:2 http://ftpmaster.internal/ubuntu plucky/universe trinityrnaseq 2.15.1+dfsg-5build1 (tar) [307 MB]
633s Get:3 http://ftpmaster.internal/ubuntu plucky/universe trinityrnaseq 2.15.1+dfsg-5build1 (diff) [39.4 kB]
633s gpgv: Signature made Sun Apr 14 18:57:26 2024 UTC
633s gpgv:                using RSA key AC0A4FF12611B6FCCF01C111393587D97D86500B
633s gpgv: Can't check signature: No public key
633s dpkg-source: warning: cannot verify inline signature for ./trinityrnaseq_2.15.1+dfsg-5build1.dsc: no acceptable signature found
639s autopkgtest [14:08:25]: testing package trinityrnaseq version 2.15.1+dfsg-5build1
639s autopkgtest [14:08:25]: build not needed
643s autopkgtest [14:08:29]: test run-tests: preparing testbed
644s Reading package lists...
644s Building dependency tree...
644s Reading state information...
644s Starting pkgProblemResolver with broken count: 0
644s Starting 2 pkgProblemResolver with broken count: 0
644s Done
645s The following additional packages will be installed:
645s   adwaita-icon-theme at-spi2-common berkeley-express bowtie bowtie2
645s   ca-certificates-java dconf-gsettings-backend dconf-service default-jre
645s   default-jre-headless fontconfig fontconfig-config fonts-dejavu-core
645s   fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings
645s   fonts-lmodern fonts-mathjax gtk-update-icon-cache hicolor-icon-theme hisat2
645s   humanity-icon-theme jaligner java-common javascript-common jellyfish
645s   kallisto libapache-pom-java libasan8 libasound2-data libasound2t64
645s   libatinject-jsr330-api-java libatk-bridge2.0-0t64 libatk1.0-0t64
645s   libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3
645s   libbamtools2.5.2 libbarclay-java libbibtex-parser-perl libblas3 libboost-dev
645s   libboost-filesystem1.83.0 libboost-iostreams1.83.0
645s   libboost-program-options1.83.0 libboost-thread1.83.0 libboost1.83-dev
645s   libcairo-gobject2 libcairo2 libclone-perl libcolord2 libcommons-codec-java
645s   libcommons-compress-java libcommons-io-java libcommons-jexl2-java
645s   libcommons-lang3-java libcommons-logging-java libcommons-math3-java
645s   libcommons-parent-java libcups2t64 libdatrie1 libdconf1 libdeflate0
645s   libdrm-amdgpu1 libdrm-intel1 libdrm-radeon1 libencode-locale-perl libepoxy0
645s   liberror-prone-java libfile-listing-perl libfontconfig1 libfreemarker-java
645s   libgatk-native-bindings-java libgbm1 libgcc-14-dev libgdk-pixbuf-2.0-0
645s   libgdk-pixbuf2.0-common libgetopt-java libgfortran5 libgif7 libgkl-java
645s   libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1
645s   libgoogle-gson-java libgraphite2-3 libgtk-3-0t64 libgtk-3-common
645s   libguava-java libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl
645s   libhtml-tree-perl libhts3t64 libhtscodecs2 libhtsjdk-java
645s   libhttp-cookies-perl libhttp-date-perl libhttp-message-perl
645s   libhttp-negotiate-perl libhttpclient-java libhttpcore-java libhwasan0
645s   libhwloc15 libice6 libio-html-perl libio-socket-ssl-perl libio-string-perl
645s   libitm1 libjbig0 libjbzip2-java libjellyfish-2.0-2 libjemalloc2
645s   libjoptsimple-java libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootstrap4
645s   libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery
645s   libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json
645s   libjs-lunr libjs-mathjax libjs-microplugin.js libjs-modernizr
645s   libjs-popper.js libjs-prettify libjs-sifter.js libjs-sphinxdoc
645s   libjs-twitter-bootstrap-datepicker libjs-underscore libjsr305-java
645s   libjung-free-java libkpathsea6 liblapack3 liblatex-tounicode-perl liblcms2-2
645s   liblerc4 liblightcouch-java liblog4j2-java liblsan0 liblua5.4-0
645s   liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto7t64
645s   libmbedtls14t64 libmbedx509-1t64 libmjson-java libmongodb-java libmpfi0
645s   libncbi-ngs3 libncbi-vdb3 libnet-http-perl libnet-ssleay-perl libngs-java
645s   libngs-jni libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
645s   libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libpicard-java
645s   libpixman-1-0 libpotrace0 libprotobuf32t64 libptexenc1 libquadmath0
645s   librhino-java libsharpyuv0 libslf4j-java libsm6 libsnappy-java libsnappy-jni
645s   libsnappy1v5 libstaden-read14t64 libstdc++-14-dev libsynctex2 libtbb12
645s   libtbbbind-2-5 libtbbmalloc2 libtcl8.6 libteckit0 libtexlua53-5 libthai-data
645s   libthai0 libtiff6 libtimedate-perl libtk8.6 libtry-tiny-perl libtsan2
645s   libubsan1 liburi-perl libvulkan1 libwayland-client0 libwayland-cursor0
645s   libwayland-egl1 libwayland-server0 libwebp7 libwww-perl
645s   libwww-robotrules-perl libx11-xcb1 libxaw7 libxcb-dri2-0 libxcb-dri3-0
645s   libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0
645s   libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxcursor1 libxdamage1
645s   libxfixes3 libxft2 libxi6 libxinerama1 libxmu6 libxpm4 libxrandr2
645s   libxrender1 libxshmfence1 libxss1 libxt6t64 libxtst6 libxxf86vm1
645s   libzzip-0-13t64 littler mesa-libgallium ncbi-blast+ ncbi-data ncbi-vdb-data
645s   node-bootstrap-sass node-html5shiv node-normalize.css openjdk-21-jre
645s   openjdk-21-jre-headless pandoc pandoc-data parafly perl-openssl-defaults
645s   python3-hisat2 python3-htseq python3-numpy python3-pysam r-base-core
645s   r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache
645s   r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biocstyle
645s   r-bioc-biocversion r-bioc-biomart r-bioc-biostrings r-bioc-delayedarray
645s   r-bioc-deseq2 r-bioc-dexseq r-bioc-edger r-bioc-genefilter
645s   r-bioc-genelendatabase r-bioc-geneplotter r-bioc-genomeinfodb
645s   r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures
645s   r-bioc-genomicranges r-bioc-go.db r-bioc-goseq r-bioc-iranges
645s   r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics r-bioc-qvalue
645s   r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays
645s   r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment
645s   r-bioc-txdbmaker r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc
645s   r-cran-abind r-cran-argparse r-cran-askpass r-cran-backports
645s   r-cran-base64enc r-cran-bh r-cran-biasedurn r-cran-biocmanager r-cran-bit
645s   r-cran-bit64 r-cran-bitops r-cran-blob r-cran-bookdown r-cran-broom
645s   r-cran-bslib r-cran-cachem r-cran-callr r-cran-cellranger r-cran-cli
645s   r-cran-clipr r-cran-cluster r-cran-codetools r-cran-colorspace
645s   r-cran-commonmark r-cran-conflicted r-cran-cpp11 r-cran-crayon r-cran-curl
645s   r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr
645s   r-cran-dtplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver
645s   r-cran-fastcluster r-cran-fastmap r-cran-filelock r-cran-findpython
645s   r-cran-fontawesome r-cran-forcats r-cran-formatr r-cran-fs
645s   r-cran-futile.logger r-cran-futile.options r-cran-gargle r-cran-generics
645s   r-cran-ggdendro r-cran-ggplot2 r-cran-glue r-cran-googledrive
645s   r-cran-googlesheets4 r-cran-goplot r-cran-gridextra r-cran-gtable
645s   r-cran-haven r-cran-highr r-cran-hms r-cran-htmltools r-cran-httpuv
645s   r-cran-httr r-cran-httr2 r-cran-hwriter r-cran-ids r-cran-isoband
645s   r-cran-jquerylib r-cran-jsonlite r-cran-kernsmooth r-cran-knitr
645s   r-cran-labeling r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lifecycle
645s   r-cran-littler r-cran-locfit r-cran-lubridate r-cran-magrittr r-cran-mass
645s   r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime
645s   r-cran-modelr r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar
645s   r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-plyr r-cran-png
645s   r-cran-prettyunits r-cran-processx r-cran-progress r-cran-promises r-cran-ps
645s   r-cran-purrr r-cran-r6 r-cran-ragg r-cran-rappdirs r-cran-rcolorbrewer
645s   r-cran-rcpp r-cran-rcpparmadillo r-cran-rcurl r-cran-readr r-cran-readxl
645s   r-cran-rematch r-cran-rematch2 r-cran-reprex r-cran-reshape2 r-cran-restfulr
645s   r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-rstudioapi
645s   r-cran-rvest r-cran-sass r-cran-scales r-cran-selectr r-cran-shiny
645s   r-cran-snow r-cran-sourcetools r-cran-statmod r-cran-stringi r-cran-stringr
645s   r-cran-survival r-cran-sys r-cran-systemfonts r-cran-textshaping
645s   r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tidyverse
645s   r-cran-timechange r-cran-tinytex r-cran-tzdb r-cran-utf8 r-cran-uuid
645s   r-cran-vctrs r-cran-viridislite r-cran-vroom r-cran-withr r-cran-xfun
645s   r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml rsem salmon samtools
645s   subread t1utils tex-common texlive-base texlive-bibtex-extra
645s   texlive-binaries texlive-latex-base trimmomatic trinityrnaseq
645s   trinityrnaseq-examples ubuntu-mono unzip x11-common xdg-utils zip zlib1g-dev
645s Suggested packages:
645s   bowtie-examples bowtie2-examples apache2 | lighttpd | httpd alsa-utils
645s   libasound2-plugins libatinject-jsr330-api-java-doc libboost-doc
645s   libboost1.83-doc libboost-atomic1.83-dev libboost-chrono1.83-dev
645s   libboost-container1.83-dev libboost-context1.83-dev
645s   libboost-contract1.83-dev libboost-coroutine1.83-dev
645s   libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev
645s   libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev
645s   libboost-graph1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev
645s   libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev
645s   libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev
645s   libboost-numpy1.83-dev libboost-program-options1.83-dev
645s   libboost-python1.83-dev libboost-random1.83-dev libboost-regex1.83-dev
645s   libboost-serialization1.83-dev libboost-stacktrace1.83-dev
645s   libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev
645s   libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev
645s   libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev
645s   colord libasm-java libxz-java libavalon-framework-java
645s   libexcalibur-logkit-java liblog4j1.2-java cups-common jython libdom4j-java
645s   libjaxen-java libjdom1-java libxalan2-java libgoogle-gson-java-doc gvfs
645s   libdata-dump-perl picard-tools libio-compress-brotli-perl
645s   libhwloc-contrib-plugins libjoptsimple-java-doc libjs-jquery-ui-docs
645s   fonts-mathjax-extras fonts-stix libjs-mathjax-doc libjsr305-java-doc
645s   liblcms2-utils libactivation-java libcommons-csv-java
645s   libconversant-disruptor-java libdisruptor-java libgeronimo-jms-1.1-spec-java
645s   libjackson2-dataformat-xml-java libjackson2-dataformat-yaml libjansi-java
645s   libjctools-java libjeromq-java libmail-java libwoodstox-java
645s   libcrypt-ssleay-perl libmpfi-doc libngs-java-doc pcscd rhino
645s   libstdc++-14-doc tcl8.6 tk8.6 libsub-name-perl libbusiness-isbn-perl
645s   libregexp-ipv6-perl libauthen-ntlm-perl nodejs libnss-mdns
645s   fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho
645s   fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic texlive-latex-recommended
645s   texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra context
645s   wkhtmltopdf librsvg2-bin groff ghc php python ruby libjs-katex
645s   citation-style-language-styles debhelper gcc gfortran python-numpy-doc
645s   python3-dev python3-pytest elpa-ess r-doc-info | r-doc-pdf r-mathlib
645s   r-base-html r-bioc-org.hs.eg.db r-cran-runit r-bioc-graph r-bioc-all
645s   r-cran-testthat r-bioc-affy r-cran-foreach r-cran-bbmisc r-cran-doparallel
645s   r-bioc-variantannotation r-bioc-shortread r-cran-batchtools r-cran-mockery
645s   r-cran-httptest2 r-bioc-bsgenome r-bioc-pwalign r-bioc-hdf5array
645s   r-cran-lobstr r-bioc-delayedmatrixstats r-cran-pheatmap r-bioc-tximport
645s   r-bioc-tximeta r-bioc-tximportdata r-cran-pbapply r-bioc-glmgampoi
645s   r-cran-roxygen2 r-bioc-rhdf5 r-cran-seuratobject r-cran-class r-cran-r.utils
645s   r-bioc-ensembldb r-bioc-annotationfilter r-cran-markdown r-bioc-gviz
645s   r-bioc-annotationhub r-cran-ellipse r-cran-gplots r-bioc-sparsematrixstats
645s   r-cran-rmariadb r-cran-ff r-cran-covr r-cran-kernlab r-cran-mvtnorm
645s   r-cran-vcd r-cran-shinyjs r-cran-jpeg r-cran-viridis r-cran-rmysql
645s   r-cran-bench r-cran-waldo r-cran-reticulate r-cran-spelling r-cran-magick
645s   r-cran-sf r-cran-getopt r-cran-interp r-cran-gam r-cran-formattable
645s   r-cran-nanotime r-cran-palmerpenguins r-cran-units r-cran-vdiffr
645s   r-cran-inline r-cran-rmpi r-cran-rlecuyer r-cran-brio r-cran-here
645s   r-cran-pkgbuild r-cran-pkgload r-cran-mockr r-cran-plm r-cran-zoo
645s   r-bioc-ebseq cwltool ghostscript gv | postscript-viewer perl-tk xpdf
645s   | pdf-viewer xzdec texlive-binaries-sse2 hintview texlive-latex-base-doc
645s   wp2latex collectl transdecoder
645s Recommended packages:
645s   librsvg2-common med-config bcftools alsa-ucm-conf alsa-topology-conf
645s   at-spi2-core libgdk-pixbuf2.0-bin libgkl-jni libgl1-amber-dri libgtk-3-bin
645s   libhtml-format-perl libhwloc-plugins node-jquery mesa-vulkan-drivers
645s   | vulkan-icd libdata-dump-perl libhtml-form-perl libhttp-daemon-perl
645s   libmailtools-perl libatk-wrapper-java-jni fonts-dejavu-extra r-recommended
645s   r-base-dev r-doc-html r-cran-testthat r-cran-remotes r-cran-downlit
645s   r-cran-htmlwidgets r-cran-miniui r-cran-rsconnect r-cran-testit r-cran-tufte
645s   r-cran-webshot r-cran-aer r-cran-bbmle r-cran-boot r-cran-car r-cran-cardata
645s   r-cran-caret r-cran-cmprsk r-cran-coda r-cran-covr r-cran-e1071
645s   r-cran-emmeans r-cran-epir r-cran-gam r-cran-gee r-cran-geepack
645s   r-cran-glmnet r-cran-gmm r-cran-hmisc r-cran-irlba r-cran-interp r-cran-ks
645s   r-cran-lavaan r-cran-leaps r-cran-lme4 r-cran-lmtest r-cran-lsmeans
645s   r-cran-maps r-cran-mclust r-cran-metafor r-cran-modeldata r-cran-multcomp
645s   r-cran-network r-cran-nnet r-cran-ordinal r-cran-plm r-cran-psych
645s   r-cran-quantreg r-cran-robust r-cran-robustbase r-cran-rsample
645s   r-cran-sandwich r-cran-spdep r-cran-spatialreg r-cran-spelling r-cran-survey
645s   r-cran-systemfit r-cran-tseries r-cran-zoo r-cran-future r-cran-thematic
645s   r-cran-mockery r-cran-rprojroot r-cran-whoami r-cran-pkgload r-cran-bench
645s   r-cran-brio r-cran-decor r-cran-desc r-cran-lobstr r-cran-webutils
645s   r-cran-r.utils r-cran-xts r-cran-markdown r-cran-rpostgresql r-cran-rmysql
645s   r-cran-unitizer r-cran-rsvg r-cran-sodium r-cran-rpart r-cran-hexbin
645s   r-cran-mapproj r-cran-profvis r-cran-sf r-cran-svglite r-cran-vdiffr
645s   r-cran-waldo r-cran-mockr r-cran-cairo r-cran-jpeg r-cran-docopt
645s   r-cran-webfakes r-cran-r.rsp r-cran-gridsvg r-cran-magick r-cran-reticulate
645s   r-cran-rgl r-cran-tikzdevice node-highlight.js r-cran-lintr r-cran-r.devices
645s   r-cran-doparallel r-cran-foreach r-cran-iterators r-cran-itertools
645s   r-cran-pingr r-cran-sessioninfo r-cran-runit r-cran-usethis r-cran-dygraphs
645s   r-cran-dbitest r-cran-gert r-cran-gh r-cran-dichromat r-cran-dt
645s   r-cran-formattable r-cran-pkgdown r-cran-zeallot r-cran-renv lmodern dvisvgm
645s   picard-tools tabix gmap rna-star r-bioc-rots r-bioc-ctc r-cran-gplots
645s   r-cran-ape libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl
645s   x11-utils x11-xserver-utils
645s The following NEW packages will be installed:
645s   adwaita-icon-theme at-spi2-common autopkgtest-satdep berkeley-express bowtie
645s   bowtie2 ca-certificates-java dconf-gsettings-backend dconf-service
645s   default-jre default-jre-headless fontconfig fontconfig-config
645s   fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome
645s   fonts-glyphicons-halflings fonts-lmodern fonts-mathjax gtk-update-icon-cache
645s   hicolor-icon-theme hisat2 humanity-icon-theme jaligner java-common
645s   javascript-common jellyfish kallisto libapache-pom-java libasan8
645s   libasound2-data libasound2t64 libatinject-jsr330-api-java
645s   libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 libavahi-client3
645s   libavahi-common-data libavahi-common3 libbamtools2.5.2 libbarclay-java
645s   libbibtex-parser-perl libblas3 libboost-dev libboost-filesystem1.83.0
645s   libboost-iostreams1.83.0 libboost-program-options1.83.0
645s   libboost-thread1.83.0 libboost1.83-dev libcairo-gobject2 libcairo2
645s   libclone-perl libcolord2 libcommons-codec-java libcommons-compress-java
645s   libcommons-io-java libcommons-jexl2-java libcommons-lang3-java
645s   libcommons-logging-java libcommons-math3-java libcommons-parent-java
645s   libcups2t64 libdatrie1 libdconf1 libdeflate0 libdrm-amdgpu1 libdrm-intel1
645s   libdrm-radeon1 libencode-locale-perl libepoxy0 liberror-prone-java
645s   libfile-listing-perl libfontconfig1 libfreemarker-java
645s   libgatk-native-bindings-java libgbm1 libgcc-14-dev libgdk-pixbuf-2.0-0
645s   libgdk-pixbuf2.0-common libgetopt-java libgfortran5 libgif7 libgkl-java
645s   libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1
645s   libgoogle-gson-java libgraphite2-3 libgtk-3-0t64 libgtk-3-common
645s   libguava-java libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl
645s   libhtml-tree-perl libhts3t64 libhtscodecs2 libhtsjdk-java
645s   libhttp-cookies-perl libhttp-date-perl libhttp-message-perl
645s   libhttp-negotiate-perl libhttpclient-java libhttpcore-java libhwasan0
645s   libhwloc15 libice6 libio-html-perl libio-socket-ssl-perl libio-string-perl
645s   libitm1 libjbig0 libjbzip2-java libjellyfish-2.0-2 libjemalloc2
645s   libjoptsimple-java libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootstrap4
645s   libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery
645s   libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json
645s   libjs-lunr libjs-mathjax libjs-microplugin.js libjs-modernizr
645s   libjs-popper.js libjs-prettify libjs-sifter.js libjs-sphinxdoc
645s   libjs-twitter-bootstrap-datepicker libjs-underscore libjsr305-java
645s   libjung-free-java libkpathsea6 liblapack3 liblatex-tounicode-perl liblcms2-2
645s   liblerc4 liblightcouch-java liblog4j2-java liblsan0 liblua5.4-0
645s   liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto7t64
645s   libmbedtls14t64 libmbedx509-1t64 libmjson-java libmongodb-java libmpfi0
645s   libncbi-ngs3 libncbi-vdb3 libnet-http-perl libnet-ssleay-perl libngs-java
645s   libngs-jni libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
645s   libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libpicard-java
645s   libpixman-1-0 libpotrace0 libprotobuf32t64 libptexenc1 libquadmath0
645s   librhino-java libsharpyuv0 libslf4j-java libsm6 libsnappy-java libsnappy-jni
645s   libsnappy1v5 libstaden-read14t64 libstdc++-14-dev libsynctex2 libtbb12
645s   libtbbbind-2-5 libtbbmalloc2 libtcl8.6 libteckit0 libtexlua53-5 libthai-data
645s   libthai0 libtiff6 libtimedate-perl libtk8.6 libtry-tiny-perl libtsan2
645s   libubsan1 liburi-perl libvulkan1 libwayland-client0 libwayland-cursor0
645s   libwayland-egl1 libwayland-server0 libwebp7 libwww-perl
645s   libwww-robotrules-perl libx11-xcb1 libxaw7 libxcb-dri2-0 libxcb-dri3-0
645s   libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0
645s   libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxcursor1 libxdamage1
645s   libxfixes3 libxft2 libxi6 libxinerama1 libxmu6 libxpm4 libxrandr2
645s   libxrender1 libxshmfence1 libxss1 libxt6t64 libxtst6 libxxf86vm1
645s   libzzip-0-13t64 littler mesa-libgallium ncbi-blast+ ncbi-data ncbi-vdb-data
645s   node-bootstrap-sass node-html5shiv node-normalize.css openjdk-21-jre
645s   openjdk-21-jre-headless pandoc pandoc-data parafly perl-openssl-defaults
645s   python3-hisat2 python3-htseq python3-numpy python3-pysam r-base-core
645s   r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache
645s   r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biocstyle
645s   r-bioc-biocversion r-bioc-biomart r-bioc-biostrings r-bioc-delayedarray
645s   r-bioc-deseq2 r-bioc-dexseq r-bioc-edger r-bioc-genefilter
645s   r-bioc-genelendatabase r-bioc-geneplotter r-bioc-genomeinfodb
645s   r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures
645s   r-bioc-genomicranges r-bioc-go.db r-bioc-goseq r-bioc-iranges
645s   r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics r-bioc-qvalue
645s   r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays
645s   r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment
645s   r-bioc-txdbmaker r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc
645s   r-cran-abind r-cran-argparse r-cran-askpass r-cran-backports
645s   r-cran-base64enc r-cran-bh r-cran-biasedurn r-cran-biocmanager r-cran-bit
645s   r-cran-bit64 r-cran-bitops r-cran-blob r-cran-bookdown r-cran-broom
645s   r-cran-bslib r-cran-cachem r-cran-callr r-cran-cellranger r-cran-cli
645s   r-cran-clipr r-cran-cluster r-cran-codetools r-cran-colorspace
645s   r-cran-commonmark r-cran-conflicted r-cran-cpp11 r-cran-crayon r-cran-curl
645s   r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr
645s   r-cran-dtplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver
645s   r-cran-fastcluster r-cran-fastmap r-cran-filelock r-cran-findpython
645s   r-cran-fontawesome r-cran-forcats r-cran-formatr r-cran-fs
645s   r-cran-futile.logger r-cran-futile.options r-cran-gargle r-cran-generics
645s   r-cran-ggdendro r-cran-ggplot2 r-cran-glue r-cran-googledrive
645s   r-cran-googlesheets4 r-cran-goplot r-cran-gridextra r-cran-gtable
645s   r-cran-haven r-cran-highr r-cran-hms r-cran-htmltools r-cran-httpuv
645s   r-cran-httr r-cran-httr2 r-cran-hwriter r-cran-ids r-cran-isoband
645s   r-cran-jquerylib r-cran-jsonlite r-cran-kernsmooth r-cran-knitr
645s   r-cran-labeling r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lifecycle
645s   r-cran-littler r-cran-locfit r-cran-lubridate r-cran-magrittr r-cran-mass
645s   r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime
645s   r-cran-modelr r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar
645s   r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-plyr r-cran-png
645s   r-cran-prettyunits r-cran-processx r-cran-progress r-cran-promises r-cran-ps
645s   r-cran-purrr r-cran-r6 r-cran-ragg r-cran-rappdirs r-cran-rcolorbrewer
645s   r-cran-rcpp r-cran-rcpparmadillo r-cran-rcurl r-cran-readr r-cran-readxl
645s   r-cran-rematch r-cran-rematch2 r-cran-reprex r-cran-reshape2 r-cran-restfulr
645s   r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-rstudioapi
645s   r-cran-rvest r-cran-sass r-cran-scales r-cran-selectr r-cran-shiny
645s   r-cran-snow r-cran-sourcetools r-cran-statmod r-cran-stringi r-cran-stringr
645s   r-cran-survival r-cran-sys r-cran-systemfonts r-cran-textshaping
645s   r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tidyverse
645s   r-cran-timechange r-cran-tinytex r-cran-tzdb r-cran-utf8 r-cran-uuid
645s   r-cran-vctrs r-cran-viridislite r-cran-vroom r-cran-withr r-cran-xfun
645s   r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml rsem salmon samtools
645s   subread t1utils tex-common texlive-base texlive-bibtex-extra
645s   texlive-binaries texlive-latex-base trimmomatic trinityrnaseq
645s   trinityrnaseq-examples ubuntu-mono unzip x11-common xdg-utils zip zlib1g-dev
645s 0 upgraded, 474 newly installed, 0 to remove and 0 not upgraded.
645s Need to get 989 MB/989 MB of archives.
645s After this operation, 2398 MB of additional disk space will be used.
645s Get:1 /tmp/autopkgtest.vWCmNc/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [828 B]
645s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [7888 B]
645s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB]
645s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
645s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.21-1 [49.8 kB]
645s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
645s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB]
645s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB]
645s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB]
645s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB]
645s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1 [147 kB]
645s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 gtk-update-icon-cache amd64 4.16.2+ds-2 [51.1 kB]
645s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 hicolor-icon-theme all 0.18-1 [13.5 kB]
645s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 humanity-icon-theme all 0.6.16 [1282 kB]
645s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-mono all 24.04-0ubuntu1 [151 kB]
645s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 adwaita-icon-theme all 47.0-1 [525 kB]
645s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 at-spi2-common all 2.54.0-1 [8774 B]
645s Get:18 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6 [141 kB]
645s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-3.2ubuntu2 [286 kB]
645s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-program-options1.83.0 amd64 1.83.0-3.2ubuntu2 [322 kB]
645s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-thread1.83.0 amd64 1.83.0-3.2ubuntu2 [278 kB]
645s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libprotobuf32t64 amd64 3.21.12-9ubuntu1 [941 kB]
646s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 berkeley-express amd64 1.5.3+dfsg-3build5 [210 kB]
646s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 ca-certificates-java all 20240118 [11.6 kB]
646s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libdconf1 amd64 0.40.0-4build2 [39.4 kB]
646s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-service amd64 0.40.0-4build2 [27.5 kB]
646s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-gsettings-backend amd64 0.40.0-4build2 [22.1 kB]
646s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 java-common all 0.76 [6852 B]
646s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.14-2build1 [161 kB]
646s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcsclite1 amd64 2.3.0-1 [23.9 kB]
646s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 openjdk-21-jre-headless amd64 21.0.5+11-1 [46.4 MB]
647s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 default-jre-headless amd64 2:1.21-76 [3178 B]
647s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libatk1.0-0t64 amd64 2.54.0-1 [55.1 kB]
647s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB]
647s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libatspi2.0-0t64 amd64 2.54.0-1 [79.6 kB]
647s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libatk-bridge2.0-0t64 amd64 2.54.0-1 [66.3 kB]
647s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
647s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
647s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB]
647s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB]
647s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.42.2-1build1 [279 kB]
647s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB]
647s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B]
647s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB]
647s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB]
647s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo-gobject2 amd64 1.18.2-2 [127 kB]
647s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libcolord2 amd64 1.4.7-1build2 [149 kB]
647s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common-data amd64 0.8-13ubuntu6 [29.7 kB]
647s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common3 amd64 0.8-13ubuntu6 [23.3 kB]
647s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-client3 amd64 0.8-13ubuntu6 [26.8 kB]
647s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libcups2t64 amd64 2.4.10-1ubuntu2 [271 kB]
647s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libepoxy0 amd64 1.5.10-1build1 [220 kB]
647s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
647s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 9.0.0-1 [487 kB]
647s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB]
647s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB]
647s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB]
647s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB]
647s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.54.0+ds-2 [235 kB]
647s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-2 [49.1 kB]
647s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-2 [28.8 kB]
647s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-client0 amd64 1.23.0-1 [27.1 kB]
647s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-cursor0 amd64 1.23.0-1 [10.8 kB]
647s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-egl1 amd64 1.23.0-1 [5662 B]
647s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcomposite1 amd64 1:0.4.5-1build3 [6320 B]
647s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libxfixes3 amd64 1:6.0.0-2build1 [10.8 kB]
647s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcursor1 amd64 1:1.2.2-1 [20.9 kB]
647s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libxdamage1 amd64 1:1.1.6-1build1 [6150 B]
647s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libxinerama1 amd64 2:1.1.4-3build1 [6396 B]
647s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrandr2 amd64 2:1.5.4-1 [19.6 kB]
647s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-3-common all 3.24.43-3ubuntu2 [1202 kB]
647s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-3-0t64 amd64 3.24.43-3ubuntu2 [2927 kB]
647s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libglvnd0 amd64 1.7.0-1build1 [69.6 kB]
647s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libglapi-mesa amd64 24.2.3-1ubuntu1 [42.4 kB]
647s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libx11-xcb1 amd64 2:1.8.7-1build1 [7800 B]
647s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-dri2-0 amd64 1.17.0-2 [7222 B]
647s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-dri3-0 amd64 1.17.0-2 [7508 B]
647s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-glx0 amd64 1.17.0-2 [24.8 kB]
647s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-present0 amd64 1.17.0-2 [6064 B]
647s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-randr0 amd64 1.17.0-2 [17.9 kB]
647s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-sync1 amd64 1.17.0-2 [9312 B]
647s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-xfixes0 amd64 1.17.0-2 [10.2 kB]
647s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libxshmfence1 amd64 1.3-1build5 [4764 B]
647s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libxxf86vm1 amd64 1:1.1.4-1build4 [9282 B]
647s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-amdgpu1 amd64 2.4.122-1 [20.9 kB]
647s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB]
647s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-intel1 amd64 2.4.122-1 [64.6 kB]
647s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-radeon1 amd64 2.4.122-1 [21.0 kB]
647s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 mesa-libgallium amd64 24.2.3-1ubuntu1 [9904 kB]
647s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 libvulkan1 amd64 1.3.290.0-1 [143 kB]
647s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-server0 amd64 1.23.0-1 [35.1 kB]
647s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libgbm1 amd64 24.2.3-1ubuntu1 [32.0 kB]
647s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 libgl1-mesa-dri amd64 24.2.3-1ubuntu1 [34.4 kB]
647s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 libglx-mesa0 amd64 24.2.3-1ubuntu1 [153 kB]
647s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 libglx0 amd64 1.7.0-1build1 [38.6 kB]
647s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 libgl1 amd64 1.7.0-1build1 [102 kB]
647s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 libasound2-data all 1.2.12-1 [21.0 kB]
647s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 libasound2t64 amd64 1.2.12-1 [394 kB]
647s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 libgif7 amd64 5.2.2-1ubuntu1 [35.2 kB]
647s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
647s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 libxtst6 amd64 2:1.2.3-1.1build1 [12.6 kB]
647s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 openjdk-21-jre amd64 21.0.5+11-1 [220 kB]
647s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 default-jre amd64 2:1.21-76 [918 B]
647s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB]
647s Get:105 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB]
647s Get:106 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lmodern all 2.005-1 [4799 kB]
647s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
647s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 hisat2 amd64 2.2.1-5 [3889 kB]
647s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 jaligner all 1.0+dfsg-11 [136 kB]
647s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 javascript-common all 11+nmu1 [5936 B]
647s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.0-1build1 [98.8 kB]
647s Get:112 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libhts3t64 amd64 1.20+ds-2 [501 kB]
647s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjellyfish-2.0-2 amd64 2.3.1-3build2 [69.3 kB]
647s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 jellyfish amd64 2.3.1-3build2 [772 kB]
647s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 kallisto amd64 0.48.0+dfsg-4build1 [273 kB]
647s Get:116 http://ftpmaster.internal/ubuntu plucky/universe amd64 libapache-pom-java all 33-2 [5874 B]
647s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-7ubuntu1 [2998 kB]
647s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5348 B]
647s Get:119 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-parent-java all 56-1 [10.7 kB]
647s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-lang3-java all 3.14.0-1 [586 kB]
647s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfreemarker-java all 2.3.32-2 [1542 kB]
648s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgoogle-gson-java all 2.10.1-1 [252 kB]
648s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjoptsimple-java all 5.0.4-4 [73.1 kB]
648s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-codec-java all 1.16.0-1 [306 kB]
648s Get:125 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB]
648s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhttpcore-java all 4.4.16-1 [612 kB]
648s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhttpclient-java all 4.5.14-1 [1241 kB]
648s Get:128 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblightcouch-java all 0.2.0-1 [74.2 kB]
648s Get:129 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmongodb-java all 3.6.3-2 [1899 kB]
648s Get:130 http://ftpmaster.internal/ubuntu plucky/universe amd64 libslf4j-java all 1.7.32-1 [141 kB]
648s Get:131 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblog4j2-java all 2.19.0-2 [2294 kB]
648s Get:132 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbarclay-java all 5.0.0+dfsg-1 [108 kB]
648s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 libio-string-perl all 1.08-4 [11.1 kB]
648s Get:134 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblatex-tounicode-perl all 0.54-2 [29.0 kB]
648s Get:135 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbibtex-parser-perl all 1.04+dfsg-1 [16.7 kB]
648s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB]
648s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-7ubuntu1 [148 kB]
648s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-7ubuntu1 [29.1 kB]
648s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-7ubuntu1 [1316 kB]
648s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-7ubuntu1 [2733 kB]
648s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-7ubuntu1 [1177 kB]
648s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-7ubuntu1 [1634 kB]
648s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-7ubuntu1 [153 kB]
648s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-7ubuntu1 [2814 kB]
648s Get:145 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-7ubuntu1 [2503 kB]
648s Get:146 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost1.83-dev amd64 1.83.0-3.2ubuntu2 [10.7 MB]
648s Get:147 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-dev amd64 1.83.0.2ubuntu1 [4468 B]
648s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-3.2ubuntu2 [260 kB]
648s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 libclone-perl amd64 0.47-1 [10.7 kB]
648s Get:150 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-compress-java all 1.25.0-1 [612 kB]
648s Get:151 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-io-java all 2.16.1-1 [451 kB]
648s Get:152 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-jexl2-java all 2.1.1-6 [250 kB]
648s Get:153 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-math3-java all 3.6.1-3 [2016 kB]
648s Get:154 http://ftpmaster.internal/ubuntu plucky/main amd64 libencode-locale-perl all 1.05-3 [11.6 kB]
648s Get:155 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjsr305-java all 0.1~+svn49-11 [27.0 kB]
648s Get:156 http://ftpmaster.internal/ubuntu plucky/universe amd64 libguava-java all 32.0.1-1 [2692 kB]
648s Get:157 http://ftpmaster.internal/ubuntu plucky/universe amd64 liberror-prone-java all 2.18.0-1 [22.5 kB]
648s Get:158 http://ftpmaster.internal/ubuntu plucky/main amd64 libtimedate-perl all 2.3300-2 [34.0 kB]
648s Get:159 http://ftpmaster.internal/ubuntu plucky/main amd64 libhttp-date-perl all 6.06-1 [10.2 kB]
648s Get:160 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-listing-perl all 6.16-1 [11.3 kB]
648s Get:161 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8014 B]
648s Get:162 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgetopt-java all 1.0.14+dfsg-6 [23.0 kB]
648s Get:163 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-7ubuntu1 [909 kB]
648s Get:164 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmjson-java all 1.4.0-3 [60.4 kB]
648s Get:165 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedcrypto7t64 amd64 2.28.8-1 [209 kB]
648s Get:166 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedx509-1t64 amd64 2.28.8-1 [46.6 kB]
648s Get:167 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedtls14t64 amd64 2.28.8-1 [82.2 kB]
648s Get:168 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-vdb-data all 3.0.2+dfsg-2build2 [67.5 kB]
648s Get:169 http://ftpmaster.internal/ubuntu plucky/universe amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2build2 [1112 kB]
648s Get:170 http://ftpmaster.internal/ubuntu plucky/universe amd64 libncbi-ngs3 amd64 3.0.3+dfsg-9ubuntu1 [149 kB]
648s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 libngs-jni amd64 3.0.3+dfsg-9ubuntu1 [4848 B]
648s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 libngs-java amd64 3.0.3+dfsg-9ubuntu1 [91.1 kB]
648s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 librhino-java all 1.7.14-2.1 [1330 kB]
648s Get:174 http://ftpmaster.internal/ubuntu plucky/main amd64 libsnappy1v5 amd64 1.2.1-1 [30.4 kB]
648s Get:175 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsnappy-jni amd64 1.1.10.5-2 [6622 B]
648s Get:176 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsnappy-java all 1.1.10.5-2 [83.7 kB]
648s Get:177 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtsjdk-java all 4.1.0+dfsg-2 [1823 kB]
648s Get:178 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgkl-java all 0.8.11+dfsg-2build1 [24.9 kB]
648s Get:179 http://ftpmaster.internal/ubuntu plucky/main amd64 libhtml-tagset-perl all 3.24-1 [14.1 kB]
648s Get:180 http://ftpmaster.internal/ubuntu plucky/main amd64 liburi-perl all 5.28-1 [88.1 kB]
648s Get:181 http://ftpmaster.internal/ubuntu plucky/main amd64 libhtml-parser-perl amd64 3.83-1build1 [86.2 kB]
648s Get:182 http://ftpmaster.internal/ubuntu plucky/main amd64 libhtml-tree-perl all 5.07-3 [200 kB]
648s Get:183 http://ftpmaster.internal/ubuntu plucky/main amd64 libio-html-perl all 1.004-3 [15.9 kB]
648s Get:184 http://ftpmaster.internal/ubuntu plucky/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.1 kB]
648s Get:185 http://ftpmaster.internal/ubuntu plucky/main amd64 libhttp-message-perl all 6.46-1ubuntu1 [75.9 kB]
648s Get:186 http://ftpmaster.internal/ubuntu plucky/main amd64 libhttp-cookies-perl all 6.11-1 [18.2 kB]
648s Get:187 http://ftpmaster.internal/ubuntu plucky/main amd64 libhttp-negotiate-perl all 6.01-2 [12.4 kB]
648s Get:188 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc15 amd64 2.11.0-2 [173 kB]
648s Get:189 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.0.10-1build3 [41.4 kB]
648s Get:190 http://ftpmaster.internal/ubuntu plucky/main amd64 perl-openssl-defaults amd64 7build3 [6626 B]
648s Get:191 http://ftpmaster.internal/ubuntu plucky/main amd64 libnet-ssleay-perl amd64 1.94-2 [317 kB]
648s Get:192 http://ftpmaster.internal/ubuntu plucky/main amd64 libio-socket-ssl-perl all 2.088-1 [200 kB]
648s Get:193 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjemalloc2 amd64 5.3.0-2build1 [256 kB]
648s Get:194 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB]
648s Get:195 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-popper.js all 1.16.1+ds-6 [54.1 kB]
648s Get:196 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [537 kB]
648s Get:197 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-d3 all 3.5.17-4 [132 kB]
648s Get:198 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-es5-shim all 4.6.7-2 [39.8 kB]
648s Get:199 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB]
648s Get:200 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
648s Get:201 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB]
648s Get:202 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB]
648s Get:203 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3712 B]
648s Get:204 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB]
648s Get:205 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
648s Get:206 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-json all 0~20221030+~1.0.8-1 [20.6 kB]
648s Get:207 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-lunr all 2.3.9~dfsg-2 [66.8 kB]
648s Get:208 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-prettify all 2015.12.04+dfsg-1.1 [39.3 kB]
648s Get:209 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
649s Get:210 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-3 [157 kB]
649s Get:211 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjung-free-java all 2.1.1-2 [1471 kB]
649s Get:212 http://ftpmaster.internal/ubuntu plucky/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-4 [64.3 kB]
649s Get:213 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB]
649s Get:214 http://ftpmaster.internal/ubuntu plucky/main amd64 liblua5.4-0 amd64 5.4.6-3build2 [166 kB]
649s Get:215 http://ftpmaster.internal/ubuntu plucky/main amd64 libnet-http-perl all 6.23-1 [22.3 kB]
649s Get:216 http://ftpmaster.internal/ubuntu plucky/main amd64 libtry-tiny-perl all 0.31-2 [20.8 kB]
649s Get:217 http://ftpmaster.internal/ubuntu plucky/main amd64 libwww-robotrules-perl all 6.02-1 [12.6 kB]
649s Get:218 http://ftpmaster.internal/ubuntu plucky/main amd64 libwww-perl all 6.77-1 [138 kB]
649s Get:219 http://ftpmaster.internal/ubuntu plucky/main amd64 liblwp-protocol-https-perl all 6.14-1 [9040 B]
649s Get:220 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmpfi0 amd64 1.5.4+ds-3 [35.1 kB]
649s Get:221 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper1 amd64 1.1.29build1 [13.4 kB]
649s Get:222 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 1.1.29build1 [8650 B]
649s Get:223 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpicard-java all 3.1.1+dfsg-1 [1731 kB]
649s Get:224 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpotrace0 amd64 1.16-2build1 [17.7 kB]
649s Get:225 http://ftpmaster.internal/ubuntu plucky/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-4 [41.9 kB]
649s Get:226 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.3-1build3 [15.7 kB]
649s Get:227 http://ftpmaster.internal/ubuntu plucky/universe amd64 libstaden-read14t64 amd64 1.15.0-1.1build2 [251 kB]
649s Get:228 http://ftpmaster.internal/ubuntu plucky/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-4 [59.9 kB]
649s Get:229 http://ftpmaster.internal/ubuntu plucky/universe amd64 libtbbmalloc2 amd64 2021.12.0-1ubuntu2 [52.5 kB]
649s Get:230 http://ftpmaster.internal/ubuntu plucky/universe amd64 libtbbbind-2-5 amd64 2021.12.0-1ubuntu2 [15.4 kB]
649s Get:231 http://ftpmaster.internal/ubuntu plucky/universe amd64 libtbb12 amd64 2021.12.0-1ubuntu2 [89.3 kB]
649s Get:232 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1build1 [988 kB]
649s Get:233 http://ftpmaster.internal/ubuntu plucky/universe amd64 libteckit0 amd64 2.5.12+ds1-1 [411 kB]
649s Get:234 http://ftpmaster.internal/ubuntu plucky/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-4 [123 kB]
649s Get:235 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB]
649s Get:236 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B]
649s Get:237 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.14-1build1 [779 kB]
649s Get:238 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB]
649s Get:239 http://ftpmaster.internal/ubuntu plucky/main amd64 libxmu6 amd64 2:1.1.3-3build2 [47.6 kB]
649s Get:240 http://ftpmaster.internal/ubuntu plucky/main amd64 libxpm4 amd64 1:3.5.17-1build2 [36.5 kB]
649s Get:241 http://ftpmaster.internal/ubuntu plucky/main amd64 libxaw7 amd64 2:1.0.14-1build2 [187 kB]
649s Get:242 http://ftpmaster.internal/ubuntu plucky/universe amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.2build1 [28.1 kB]
649s Get:243 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14 [174 kB]
649s Get:244 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB]
649s Get:245 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-0ubuntu1 [67.5 kB]
649s Get:246 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.1-1 [28.5 MB]
649s Get:247 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-littler amd64 0.3.20-1 [96.0 kB]
649s Get:248 http://ftpmaster.internal/ubuntu plucky/universe amd64 littler all 0.3.20-1 [2486 B]
649s Get:249 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-data all 6.1.20170106+dfsg2-3 [3966 kB]
649s Get:250 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-blast+ amd64 2.16.0+ds-6 [15.2 MB]
649s Get:251 http://ftpmaster.internal/ubuntu plucky/universe amd64 node-bootstrap-sass all 3.4.3-2 [187 kB]
649s Get:252 http://ftpmaster.internal/ubuntu plucky/universe amd64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB]
649s Get:253 http://ftpmaster.internal/ubuntu plucky/universe amd64 node-normalize.css all 8.0.1-5 [10.8 kB]
649s Get:254 http://ftpmaster.internal/ubuntu plucky/universe amd64 pandoc-data all 3.1.11.1-3 [78.7 kB]
649s Get:255 http://ftpmaster.internal/ubuntu plucky/universe amd64 pandoc amd64 3.1.11.1+ds-2 [27.2 MB]
649s Get:256 http://ftpmaster.internal/ubuntu plucky/universe amd64 parafly amd64 0.1.0-4 [16.5 kB]
649s Get:257 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-hisat2 all 2.2.1-5 [12.7 kB]
649s Get:258 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB]
649s Get:259 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB]
650s Get:260 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-htseq amd64 2.0.5-2 [319 kB]
650s Get:261 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocgenerics all 0.50.0-2 [605 kB]
650s Get:262 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biobase amd64 2.64.0-4 [2154 kB]
650s Get:263 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-s4vectors amd64 0.42.1+dfsg-2 [1890 kB]
650s Get:264 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-iranges amd64 2.38.1-1 [2298 kB]
650s Get:265 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dbi all 1.2.3-1 [853 kB]
650s Get:266 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bit amd64 4.0.5-1 [1063 kB]
650s Get:267 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bit64 amd64 4.0.5-1 [465 kB]
650s Get:268 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rlang amd64 1.1.4-1 [1708 kB]
650s Get:269 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cli amd64 3.6.2-1 [1380 kB]
650s Get:270 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-glue amd64 1.7.0-1 [154 kB]
650s Get:271 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
650s Get:272 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB]
650s Get:273 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-blob all 1.2.4-1 [49.8 kB]
650s Get:274 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fastmap amd64 1.1.1-1 [70.5 kB]
650s Get:275 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cachem amd64 1.0.8-1 [72.1 kB]
650s Get:276 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-memoise all 2.0.1-1 [53.9 kB]
650s Get:277 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
650s Get:278 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-plogr all 0.2.0-3build1 [15.1 kB]
650s Get:279 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cpp11 all 0.4.7-1 [266 kB]
650s Get:280 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rsqlite amd64 2.3.7-2 [1237 kB]
650s Get:281 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-curl amd64 5.2.1+dfsg-1 [180 kB]
650s Get:282 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-jsonlite amd64 1.8.8+dfsg-1 [441 kB]
650s Get:283 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mime amd64 0.12-2 [35.8 kB]
650s Get:284 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-sys amd64 3.4.2-1 [44.6 kB]
650s Get:285 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-askpass amd64 1.2.0-1 [24.6 kB]
650s Get:286 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-openssl amd64 2.2.0+dfsg-1 [405 kB]
650s Get:287 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r6 all 2.5.1-1 [99.0 kB]
650s Get:288 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
650s Get:289 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-png amd64 0.1-8-1build2 [40.6 kB]
650s Get:290 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB]
650s Get:291 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-zlibbioc all 1.50.0+dfsg-2 [10.1 kB]
650s Get:292 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-xvector amd64 0.44.0-1 [624 kB]
650s Get:293 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-ucsc.utils all 1.0.0+ds-2 [77.0 kB]
650s Get:294 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomeinfodbdata all 1.2.12-1 [12.6 MB]
650s Get:295 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomeinfodb all 1.40.1+dfsg-1 [3883 kB]
650s Get:296 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-crayon all 1.5.2-1 [164 kB]
650s Get:297 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biostrings amd64 2.72.1+dfsg-1 [13.2 MB]
650s Get:298 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-keggrest all 1.44.1+dfsg-1 [188 kB]
650s Get:299 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-annotationdbi all 1.66.0-1 [4848 kB]
650s Get:300 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xml amd64 3.99-0.17-1 [1745 kB]
650s Get:301 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xtable all 1:1.8-4-2 [689 kB]
650s Get:302 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-annotate all 1.82.0+dfsg-1 [1765 kB]
650s Get:303 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-generics all 0.1.3-1 [81.3 kB]
650s Get:304 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB]
650s Get:305 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fansi amd64 1.0.5-1 [619 kB]
650s Get:306 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB]
650s Get:307 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB]
650s Get:308 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [415 kB]
650s Get:309 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-withr all 3.0.0+dfsg-1 [228 kB]
650s Get:310 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [222 kB]
650s Get:311 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dplyr amd64 1.1.4-1 [1515 kB]
650s Get:312 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-purrr amd64 1.0.2-1 [502 kB]
650s Get:313 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-stringi amd64 1.8.3-1 [873 kB]
650s Get:314 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB]
650s Get:315 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB]
650s Get:316 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dbplyr all 2.4.0+dfsg-1 [1172 kB]
650s Get:317 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-filelock amd64 1.0.3-1 [29.6 kB]
650s Get:318 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocfilecache all 2.12.0+dfsg-1 [304 kB]
650s Get:319 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocio all 1.14.0+dfsg-1 [215 kB]
650s Get:320 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-formatr all 1.14-2 [152 kB]
650s Get:321 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lambda.r all 1.2.4-2build1 [119 kB]
650s Get:322 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-futile.options all 1.0.1-3build1 [20.2 kB]
650s Get:323 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-futile.logger all 1.4.3-4build1 [99.3 kB]
650s Get:324 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-snow all 1:0.4.4-2 [97.6 kB]
650s Get:325 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-codetools all 0.2-20-1 [90.5 kB]
650s Get:326 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bh all 1.84.0-1 [5962 B]
650s Get:327 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocparallel amd64 1.38.0-2 [1342 kB]
650s Get:328 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-base64enc amd64 0.1-3-3 [27.6 kB]
650s Get:329 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-digest amd64 0.6.36-1 [199 kB]
650s Get:330 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-htmltools amd64 0.5.8.1-1 [373 kB]
650s Get:331 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-evaluate all 0.24.0-1 [93.5 kB]
650s Get:332 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xfun amd64 0.45+dfsg-1 [518 kB]
650s Get:333 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB]
650s Get:334 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-yaml amd64 2.3.8-2 [108 kB]
650s Get:335 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
650s Get:336 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-knitr all 1.47+dfsg-1 [911 kB]
650s Get:337 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.5 kB]
650s Get:338 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fs amd64 1.6.4+dfsg-1 [245 kB]
650s Get:339 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rappdirs amd64 0.3.3-1 [47.5 kB]
650s Get:340 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-sass amd64 0.4.9+dfsg-1 [1001 kB]
650s Get:341 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bslib all 0.7.0+dfsg-1 [4255 kB]
650s Get:342 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fontawesome all 0.5.2-1 [1300 kB]
650s Get:343 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tinytex all 0.51-1 [145 kB]
650s Get:344 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-modernizr all 3.13.0-0.1 [101 kB]
650s Get:345 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB]
650s Get:346 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcpp amd64 1.0.13-1 [1990 kB]
650s Get:347 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-later amd64 1.3.2+dfsg-1 [123 kB]
650s Get:348 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-promises amd64 1.3.0+dfsg-1 [287 kB]
650s Get:349 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [510 kB]
650s Get:350 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-sourcetools amd64 0.1.7-1-1 [48.1 kB]
650s Get:351 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-commonmark amd64 1.9.1-1 [131 kB]
650s Get:352 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB]
650s Get:353 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-shiny all 1.8.1.1+dfsg-1 [2873 kB]
651s Get:354 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rmarkdown all 2.27+dfsg-1 [1501 kB]
651s Get:355 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bookdown all 0.40+dfsg-1 [1409 kB]
651s Get:356 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-biocmanager all 1.30.22+dfsg-2 [125 kB]
651s Get:357 http://ftpmaster.internal/ubuntu plucky/universe amd64 tex-common all 6.18 [32.8 kB]
651s Get:358 http://ftpmaster.internal/ubuntu plucky/main amd64 t1utils amd64 1.41-4build3 [61.3 kB]
651s Get:359 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-binaries amd64 2024.20240313.70630+ds-4 [8478 kB]
651s Get:360 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-base all 2024.20240706-1 [22.5 MB]
651s Get:361 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-latex-base all 2024.20240706-1 [1256 kB]
651s Get:362 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-bibtex-extra all 2024.20240706-2 [79.1 MB]
651s Get:363 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocversion all 3.19.1-1 [11.2 kB]
651s Get:364 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocstyle all 2.32.1+dfsg-1 [452 kB]
651s Get:365 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-hms all 1.1.3-1 [96.5 kB]
651s Get:366 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-prettyunits all 1.2.0-1 [162 kB]
651s Get:367 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-progress all 1.2.3-1 [91.9 kB]
651s Get:368 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-httr2 all 1.0.2-1 [571 kB]
651s Get:369 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xml2 amd64 1.3.6-1 [322 kB]
651s Get:370 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biomart all 2.60.1+dfsg-1 [431 kB]
651s Get:371 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB]
651s Get:372 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrix amd64 1.7-0-3 [4185 kB]
651s Get:373 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrixstats amd64 1.3.0-1 [505 kB]
651s Get:374 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-matrixgenerics all 1.16.0-2 [424 kB]
651s Get:375 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-abind all 1.4-5-2 [63.6 kB]
651s Get:376 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-s4arrays amd64 1.4.1+dfsg-1 [525 kB]
652s Get:377 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-sparsearray amd64 1.4.8+dfsg-1 [1254 kB]
652s Get:378 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-delayedarray amd64 0.30.1+dfsg-1 [1846 kB]
652s Get:379 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomicranges amd64 1.56.1+dfsg-1 [1840 kB]
652s Get:380 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-summarizedexperiment all 1.34.0+dfsg-1 [1134 kB]
652s Get:381 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-locfit amd64 1.5-9.9-1 [518 kB]
652s Get:382 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-gtable all 0.3.5+dfsg-1 [192 kB]
652s Get:383 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB]
652s Get:384 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mass amd64 7.3-61-1 [1109 kB]
652s Get:385 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nlme amd64 3.1.166-1 [2314 kB]
652s Get:386 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB]
652s Get:387 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB]
652s Get:388 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB]
652s Get:389 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1541 kB]
652s Get:390 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-munsell all 0.5.1-1 [213 kB]
652s Get:391 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB]
652s Get:392 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-viridislite all 0.4.2-2 [1088 kB]
652s Get:393 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-scales all 1.3.0-1 [603 kB]
652s Get:394 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB]
652s Get:395 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcpparmadillo amd64 14.0.0-1-1 [866 kB]
652s Get:396 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-deseq2 amd64 1.44.0+dfsg-1 [1236 kB]
652s Get:397 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-hwriter all 1.3.2.1-1 [106 kB]
652s Get:398 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bitops amd64 1.0-7-1 [29.8 kB]
652s Get:399 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-rhtslib amd64 3.0.0+dfsg-1 [1413 kB]
652s Get:400 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-rsamtools amd64 2.20.0+dfsg-1 [3684 kB]
652s Get:401 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-statmod amd64 1.5.0-1 [295 kB]
652s Get:402 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-geneplotter all 1.82.0+dfsg-1 [1417 kB]
652s Get:403 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-survival amd64 3.7-0-1 [6271 kB]
652s Get:404 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genefilter amd64 1.86.0-1 [1113 kB]
652s Get:405 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-dexseq all 1.50.0+dfsg-1 [452 kB]
652s Get:406 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-limma amd64 3.60.4+dfsg-1 [1955 kB]
652s Get:407 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-edger amd64 4.2.1+dfsg-1 [1181 kB]
652s Get:408 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomicalignments amd64 1.40.0-1 [2149 kB]
652s Get:409 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcurl amd64 1.98-1.14+dfsg-1build2 [793 kB]
652s Get:410 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rjson amd64 0.2.21-1 [143 kB]
652s Get:411 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-restfulr amd64 0.0.15-1 [380 kB]
652s Get:412 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-rtracklayer amd64 1.64.0-1 [5074 kB]
652s Get:413 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomicfeatures all 1.56.0+dfsg-1 [980 kB]
652s Get:414 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-txdbmaker all 1.0.1+ds-1 [875 kB]
652s Get:415 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genelendatabase all 1.40.1-1 [100 MB]
653s Get:416 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-go.db all 3.19.1-1 [17.7 MB]
653s Get:417 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-biasedurn amd64 2.0.11-1 [279 kB]
653s Get:418 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-goseq all 1.56.0-1 [1754 kB]
653s Get:419 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-plyr amd64 1.8.9-1 [832 kB]
653s Get:420 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-reshape2 amd64 1.4.4-2build1 [114 kB]
653s Get:421 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-qvalue all 2.36.0-1 [2805 kB]
653s Get:422 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-findpython all 1.0.8-1 [24.2 kB]
653s Get:423 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-argparse all 2.2.3+dfsg-1 [143 kB]
653s Get:424 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-backports amd64 1.5.0-2 [121 kB]
653s Get:425 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-broom all 1.0.6+dfsg-1 [1803 kB]
653s Get:426 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ps amd64 1.7.6-1 [313 kB]
653s Get:427 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-processx amd64 3.8.4-1 [353 kB]
653s Get:428 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-callr all 3.7.6-1 [458 kB]
653s Get:429 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rematch all 2.0.0-1 [18.3 kB]
653s Get:430 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cellranger all 1.1.0-3 [102 kB]
653s Get:431 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-clipr all 0.8.0-1 [53.5 kB]
653s Get:432 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cluster amd64 2.1.6-1build1 [553 kB]
653s Get:433 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-conflicted all 1.2.0-1.1 [60.8 kB]
653s Get:434 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-data.table amd64 1.15.4+dfsg-2.2 [1860 kB]
653s Get:435 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dtplyr all 1.3.1-1 [364 kB]
653s Get:436 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ellipsis amd64 0.3.2-2 [35.6 kB]
653s Get:437 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fastcluster amd64 1.2.6-1build1 [192 kB]
653s Get:438 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-forcats all 1.0.0-1 [369 kB]
653s Get:439 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-gargle all 1.5.2-1 [737 kB]
653s Get:440 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ggdendro all 0.2.0+dfsg-1 [173 kB]
653s Get:441 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-uuid amd64 1.2-1-1 [48.5 kB]
653s Get:442 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-googledrive all 2.1.1-1 [1224 kB]
653s Get:443 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ids all 1.0.1-2 [124 kB]
653s Get:444 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rematch2 all 2.1.2-2build1 [46.5 kB]
653s Get:445 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-googlesheets4 all 1.1.1-1 [520 kB]
653s Get:446 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-gridextra all 2.3-3build1 [1024 kB]
653s Get:447 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-goplot all 1.0.2-2 [2427 kB]
653s Get:448 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tzdb amd64 0.4.0-2 [521 kB]
653s Get:449 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-vroom amd64 1.6.5-1 [848 kB]
654s Get:450 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-readr amd64 2.1.5-1 [766 kB]
654s Get:451 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-haven amd64 2.5.4-1 [346 kB]
654s Get:452 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-kernsmooth amd64 2.23-24-1 [92.9 kB]
654s Get:453 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-timechange amd64 0.3.0-1 [178 kB]
654s Get:454 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lubridate amd64 1.9.3+dfsg-1 [1010 kB]
654s Get:455 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-modelr all 0.1.11-1 [195 kB]
654s Get:456 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-systemfonts amd64 1.1.0-1 [245 kB]
654s Get:457 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-textshaping amd64 0.3.7-2 [95.5 kB]
654s Get:458 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ragg amd64 1.3.2-1 [495 kB]
654s Get:459 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-readxl amd64 1.4.3-1 [736 kB]
654s Get:460 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rstudioapi all 0.16.0-1 [287 kB]
654s Get:461 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-reprex all 2.1.0-1 [465 kB]
654s Get:462 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-selectr all 0.4-2-2build1 [416 kB]
654s Get:463 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rvest all 1.0.4-1 [298 kB]
654s Get:464 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tidyverse all 2.0.0+dfsg-1 [84.5 kB]
654s Get:465 http://ftpmaster.internal/ubuntu plucky/universe amd64 bowtie amd64 1.3.1-3 [1562 kB]
654s Get:466 http://ftpmaster.internal/ubuntu plucky/universe amd64 bowtie2 amd64 2.5.4-1 [1336 kB]
654s Get:467 http://ftpmaster.internal/ubuntu plucky/universe amd64 rsem amd64 1.3.3+dfsg-3build1 [36.1 MB]
654s Get:468 http://ftpmaster.internal/ubuntu plucky/universe amd64 salmon amd64 1.10.2+ds1-1build2 [3308 kB]
655s Get:469 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.20-3 [599 kB]
655s Get:470 http://ftpmaster.internal/ubuntu plucky/universe amd64 subread amd64 2.0.6+dfsg-3 [613 kB]
655s Get:471 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjbzip2-java all 0.9.1-8 [42.4 kB]
655s Get:472 http://ftpmaster.internal/ubuntu plucky/universe amd64 trimmomatic all 0.39+dfsg-2 [758 kB]
655s Get:473 http://ftpmaster.internal/ubuntu plucky/universe amd64 trinityrnaseq amd64 2.15.1+dfsg-5build1 [1718 kB]
655s Get:474 http://ftpmaster.internal/ubuntu plucky/universe amd64 trinityrnaseq-examples amd64 2.15.1+dfsg-5build1 [299 MB]
660s Preconfiguring packages ...
660s Fetched 989 MB in 14s (70.8 MB/s)
660s Selecting previously unselected package libgdk-pixbuf2.0-common.
661s (Reading database ... 
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(Reading database ... 75323 files and directories currently installed.)
661s Preparing to unpack .../000-libgdk-pixbuf2.0-common_2.42.12+dfsg-1_all.deb ...
661s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ...
661s Selecting previously unselected package libjpeg-turbo8:amd64.
661s Preparing to unpack .../001-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ...
661s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ...
661s Selecting previously unselected package libjpeg8:amd64.
661s Preparing to unpack .../002-libjpeg8_8c-2ubuntu11_amd64.deb ...
661s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ...
661s Selecting previously unselected package libdeflate0:amd64.
661s Preparing to unpack .../003-libdeflate0_1.21-1_amd64.deb ...
661s Unpacking libdeflate0:amd64 (1.21-1) ...
661s Selecting previously unselected package libjbig0:amd64.
661s Preparing to unpack .../004-libjbig0_2.1-6.1ubuntu2_amd64.deb ...
661s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ...
661s Selecting previously unselected package liblerc4:amd64.
661s Preparing to unpack .../005-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ...
661s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ...
661s Selecting previously unselected package libsharpyuv0:amd64.
661s Preparing to unpack .../006-libsharpyuv0_1.4.0-0.1_amd64.deb ...
661s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ...
661s Selecting previously unselected package libwebp7:amd64.
661s Preparing to unpack .../007-libwebp7_1.4.0-0.1_amd64.deb ...
661s Unpacking libwebp7:amd64 (1.4.0-0.1) ...
661s Selecting previously unselected package libtiff6:amd64.
661s Preparing to unpack .../008-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ...
661s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ...
661s Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64.
661s Preparing to unpack .../009-libgdk-pixbuf-2.0-0_2.42.12+dfsg-1_amd64.deb ...
661s Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1) ...
661s Selecting previously unselected package gtk-update-icon-cache.
661s Preparing to unpack .../010-gtk-update-icon-cache_4.16.2+ds-2_amd64.deb ...
661s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed.
661s 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.
661s Unpacking gtk-update-icon-cache (4.16.2+ds-2) ...
661s Selecting previously unselected package hicolor-icon-theme.
661s Preparing to unpack .../011-hicolor-icon-theme_0.18-1_all.deb ...
661s Unpacking hicolor-icon-theme (0.18-1) ...
661s Selecting previously unselected package humanity-icon-theme.
661s Preparing to unpack .../012-humanity-icon-theme_0.6.16_all.deb ...
661s Unpacking humanity-icon-theme (0.6.16) ...
662s Selecting previously unselected package ubuntu-mono.
662s Preparing to unpack .../013-ubuntu-mono_24.04-0ubuntu1_all.deb ...
662s Unpacking ubuntu-mono (24.04-0ubuntu1) ...
662s Selecting previously unselected package adwaita-icon-theme.
662s Preparing to unpack .../014-adwaita-icon-theme_47.0-1_all.deb ...
662s Unpacking adwaita-icon-theme (47.0-1) ...
662s Selecting previously unselected package at-spi2-common.
662s Preparing to unpack .../015-at-spi2-common_2.54.0-1_all.deb ...
662s Unpacking at-spi2-common (2.54.0-1) ...
662s Selecting previously unselected package libbamtools2.5.2:amd64.
662s Preparing to unpack .../016-libbamtools2.5.2_2.5.2+dfsg-6_amd64.deb ...
662s Unpacking libbamtools2.5.2:amd64 (2.5.2+dfsg-6) ...
662s Selecting previously unselected package libboost-filesystem1.83.0:amd64.
662s Preparing to unpack .../017-libboost-filesystem1.83.0_1.83.0-3.2ubuntu2_amd64.deb ...
662s Unpacking libboost-filesystem1.83.0:amd64 (1.83.0-3.2ubuntu2) ...
663s Selecting previously unselected package libboost-program-options1.83.0:amd64.
663s Preparing to unpack .../018-libboost-program-options1.83.0_1.83.0-3.2ubuntu2_amd64.deb ...
663s Unpacking libboost-program-options1.83.0:amd64 (1.83.0-3.2ubuntu2) ...
663s Selecting previously unselected package libboost-thread1.83.0:amd64.
663s Preparing to unpack .../019-libboost-thread1.83.0_1.83.0-3.2ubuntu2_amd64.deb ...
663s Unpacking libboost-thread1.83.0:amd64 (1.83.0-3.2ubuntu2) ...
663s Selecting previously unselected package libprotobuf32t64:amd64.
663s Preparing to unpack .../020-libprotobuf32t64_3.21.12-9ubuntu1_amd64.deb ...
663s Unpacking libprotobuf32t64:amd64 (3.21.12-9ubuntu1) ...
663s Selecting previously unselected package berkeley-express.
663s Preparing to unpack .../021-berkeley-express_1.5.3+dfsg-3build5_amd64.deb ...
663s Unpacking berkeley-express (1.5.3+dfsg-3build5) ...
663s Selecting previously unselected package ca-certificates-java.
663s Preparing to unpack .../022-ca-certificates-java_20240118_all.deb ...
663s Unpacking ca-certificates-java (20240118) ...
663s Selecting previously unselected package libdconf1:amd64.
663s Preparing to unpack .../023-libdconf1_0.40.0-4build2_amd64.deb ...
663s Unpacking libdconf1:amd64 (0.40.0-4build2) ...
663s Selecting previously unselected package dconf-service.
663s Preparing to unpack .../024-dconf-service_0.40.0-4build2_amd64.deb ...
663s Unpacking dconf-service (0.40.0-4build2) ...
663s Selecting previously unselected package dconf-gsettings-backend:amd64.
663s Preparing to unpack .../025-dconf-gsettings-backend_0.40.0-4build2_amd64.deb ...
663s Unpacking dconf-gsettings-backend:amd64 (0.40.0-4build2) ...
663s Selecting previously unselected package java-common.
663s Preparing to unpack .../026-java-common_0.76_all.deb ...
663s Unpacking java-common (0.76) ...
663s Selecting previously unselected package liblcms2-2:amd64.
663s Preparing to unpack .../027-liblcms2-2_2.14-2build1_amd64.deb ...
663s Unpacking liblcms2-2:amd64 (2.14-2build1) ...
663s Selecting previously unselected package libpcsclite1:amd64.
663s Preparing to unpack .../028-libpcsclite1_2.3.0-1_amd64.deb ...
663s Unpacking libpcsclite1:amd64 (2.3.0-1) ...
663s Selecting previously unselected package openjdk-21-jre-headless:amd64.
663s Preparing to unpack .../029-openjdk-21-jre-headless_21.0.5+11-1_amd64.deb ...
663s Unpacking openjdk-21-jre-headless:amd64 (21.0.5+11-1) ...
664s Selecting previously unselected package default-jre-headless.
664s Preparing to unpack .../030-default-jre-headless_2%3a1.21-76_amd64.deb ...
664s Unpacking default-jre-headless (2:1.21-76) ...
664s Selecting previously unselected package libatk1.0-0t64:amd64.
664s Preparing to unpack .../031-libatk1.0-0t64_2.54.0-1_amd64.deb ...
664s Unpacking libatk1.0-0t64:amd64 (2.54.0-1) ...
664s Selecting previously unselected package libxi6:amd64.
664s Preparing to unpack .../032-libxi6_2%3a1.8.2-1_amd64.deb ...
664s Unpacking libxi6:amd64 (2:1.8.2-1) ...
664s Selecting previously unselected package libatspi2.0-0t64:amd64.
664s Preparing to unpack .../033-libatspi2.0-0t64_2.54.0-1_amd64.deb ...
664s Unpacking libatspi2.0-0t64:amd64 (2.54.0-1) ...
664s Selecting previously unselected package libatk-bridge2.0-0t64:amd64.
664s Preparing to unpack .../034-libatk-bridge2.0-0t64_2.54.0-1_amd64.deb ...
664s Unpacking libatk-bridge2.0-0t64:amd64 (2.54.0-1) ...
664s Selecting previously unselected package fonts-dejavu-mono.
664s Preparing to unpack .../035-fonts-dejavu-mono_2.37-8_all.deb ...
664s Unpacking fonts-dejavu-mono (2.37-8) ...
664s Selecting previously unselected package fonts-dejavu-core.
664s Preparing to unpack .../036-fonts-dejavu-core_2.37-8_all.deb ...
664s Unpacking fonts-dejavu-core (2.37-8) ...
664s Selecting previously unselected package fontconfig-config.
664s Preparing to unpack .../037-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ...
664s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
664s Selecting previously unselected package libfontconfig1:amd64.
664s Preparing to unpack .../038-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ...
664s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ...
664s Selecting previously unselected package libpixman-1-0:amd64.
664s Preparing to unpack .../039-libpixman-1-0_0.42.2-1build1_amd64.deb ...
664s Unpacking libpixman-1-0:amd64 (0.42.2-1build1) ...
664s Selecting previously unselected package libxcb-render0:amd64.
664s Preparing to unpack .../040-libxcb-render0_1.17.0-2_amd64.deb ...
664s Unpacking libxcb-render0:amd64 (1.17.0-2) ...
664s Selecting previously unselected package libxcb-shm0:amd64.
664s Preparing to unpack .../041-libxcb-shm0_1.17.0-2_amd64.deb ...
664s Unpacking libxcb-shm0:amd64 (1.17.0-2) ...
664s Selecting previously unselected package libxrender1:amd64.
664s Preparing to unpack .../042-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ...
664s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ...
665s Selecting previously unselected package libcairo2:amd64.
665s Preparing to unpack .../043-libcairo2_1.18.2-2_amd64.deb ...
665s Unpacking libcairo2:amd64 (1.18.2-2) ...
665s Selecting previously unselected package libcairo-gobject2:amd64.
665s Preparing to unpack .../044-libcairo-gobject2_1.18.2-2_amd64.deb ...
665s Unpacking libcairo-gobject2:amd64 (1.18.2-2) ...
665s Selecting previously unselected package libcolord2:amd64.
665s Preparing to unpack .../045-libcolord2_1.4.7-1build2_amd64.deb ...
665s Unpacking libcolord2:amd64 (1.4.7-1build2) ...
665s Selecting previously unselected package libavahi-common-data:amd64.
665s Preparing to unpack .../046-libavahi-common-data_0.8-13ubuntu6_amd64.deb ...
665s Unpacking libavahi-common-data:amd64 (0.8-13ubuntu6) ...
665s Selecting previously unselected package libavahi-common3:amd64.
665s Preparing to unpack .../047-libavahi-common3_0.8-13ubuntu6_amd64.deb ...
665s Unpacking libavahi-common3:amd64 (0.8-13ubuntu6) ...
665s Selecting previously unselected package libavahi-client3:amd64.
665s Preparing to unpack .../048-libavahi-client3_0.8-13ubuntu6_amd64.deb ...
665s Unpacking libavahi-client3:amd64 (0.8-13ubuntu6) ...
665s Selecting previously unselected package libcups2t64:amd64.
665s Preparing to unpack .../049-libcups2t64_2.4.10-1ubuntu2_amd64.deb ...
665s Unpacking libcups2t64:amd64 (2.4.10-1ubuntu2) ...
665s Selecting previously unselected package libepoxy0:amd64.
665s Preparing to unpack .../050-libepoxy0_1.5.10-1build1_amd64.deb ...
665s Unpacking libepoxy0:amd64 (1.5.10-1build1) ...
665s Selecting previously unselected package libgraphite2-3:amd64.
665s Preparing to unpack .../051-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ...
665s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
665s Selecting previously unselected package libharfbuzz0b:amd64.
665s Preparing to unpack .../052-libharfbuzz0b_9.0.0-1_amd64.deb ...
665s Unpacking libharfbuzz0b:amd64 (9.0.0-1) ...
665s Selecting previously unselected package fontconfig.
665s Preparing to unpack .../053-fontconfig_2.15.0-1.1ubuntu2_amd64.deb ...
665s Unpacking fontconfig (2.15.0-1.1ubuntu2) ...
665s Selecting previously unselected package libthai-data.
665s Preparing to unpack .../054-libthai-data_0.1.29-2build1_all.deb ...
665s Unpacking libthai-data (0.1.29-2build1) ...
665s Selecting previously unselected package libdatrie1:amd64.
665s Preparing to unpack .../055-libdatrie1_0.2.13-3build1_amd64.deb ...
665s Unpacking libdatrie1:amd64 (0.2.13-3build1) ...
665s Selecting previously unselected package libthai0:amd64.
665s Preparing to unpack .../056-libthai0_0.1.29-2build1_amd64.deb ...
665s Unpacking libthai0:amd64 (0.1.29-2build1) ...
665s Selecting previously unselected package libpango-1.0-0:amd64.
665s Preparing to unpack .../057-libpango-1.0-0_1.54.0+ds-2_amd64.deb ...
665s Unpacking libpango-1.0-0:amd64 (1.54.0+ds-2) ...
665s Selecting previously unselected package libpangoft2-1.0-0:amd64.
665s Preparing to unpack .../058-libpangoft2-1.0-0_1.54.0+ds-2_amd64.deb ...
665s Unpacking libpangoft2-1.0-0:amd64 (1.54.0+ds-2) ...
665s Selecting previously unselected package libpangocairo-1.0-0:amd64.
665s Preparing to unpack .../059-libpangocairo-1.0-0_1.54.0+ds-2_amd64.deb ...
665s Unpacking libpangocairo-1.0-0:amd64 (1.54.0+ds-2) ...
665s Selecting previously unselected package libwayland-client0:amd64.
665s Preparing to unpack .../060-libwayland-client0_1.23.0-1_amd64.deb ...
665s Unpacking libwayland-client0:amd64 (1.23.0-1) ...
665s Selecting previously unselected package libwayland-cursor0:amd64.
665s Preparing to unpack .../061-libwayland-cursor0_1.23.0-1_amd64.deb ...
665s Unpacking libwayland-cursor0:amd64 (1.23.0-1) ...
665s Selecting previously unselected package libwayland-egl1:amd64.
665s Preparing to unpack .../062-libwayland-egl1_1.23.0-1_amd64.deb ...
665s Unpacking libwayland-egl1:amd64 (1.23.0-1) ...
665s Selecting previously unselected package libxcomposite1:amd64.
665s Preparing to unpack .../063-libxcomposite1_1%3a0.4.5-1build3_amd64.deb ...
665s Unpacking libxcomposite1:amd64 (1:0.4.5-1build3) ...
665s Selecting previously unselected package libxfixes3:amd64.
665s Preparing to unpack .../064-libxfixes3_1%3a6.0.0-2build1_amd64.deb ...
665s Unpacking libxfixes3:amd64 (1:6.0.0-2build1) ...
665s Selecting previously unselected package libxcursor1:amd64.
665s Preparing to unpack .../065-libxcursor1_1%3a1.2.2-1_amd64.deb ...
665s Unpacking libxcursor1:amd64 (1:1.2.2-1) ...
665s Selecting previously unselected package libxdamage1:amd64.
665s Preparing to unpack .../066-libxdamage1_1%3a1.1.6-1build1_amd64.deb ...
665s Unpacking libxdamage1:amd64 (1:1.1.6-1build1) ...
665s Selecting previously unselected package libxinerama1:amd64.
665s Preparing to unpack .../067-libxinerama1_2%3a1.1.4-3build1_amd64.deb ...
665s Unpacking libxinerama1:amd64 (2:1.1.4-3build1) ...
665s Selecting previously unselected package libxrandr2:amd64.
665s Preparing to unpack .../068-libxrandr2_2%3a1.5.4-1_amd64.deb ...
665s Unpacking libxrandr2:amd64 (2:1.5.4-1) ...
665s Selecting previously unselected package libgtk-3-common.
665s Preparing to unpack .../069-libgtk-3-common_3.24.43-3ubuntu2_all.deb ...
665s Unpacking libgtk-3-common (3.24.43-3ubuntu2) ...
665s Selecting previously unselected package libgtk-3-0t64:amd64.
665s Preparing to unpack .../070-libgtk-3-0t64_3.24.43-3ubuntu2_amd64.deb ...
665s Unpacking libgtk-3-0t64:amd64 (3.24.43-3ubuntu2) ...
665s Selecting previously unselected package libglvnd0:amd64.
665s Preparing to unpack .../071-libglvnd0_1.7.0-1build1_amd64.deb ...
665s Unpacking libglvnd0:amd64 (1.7.0-1build1) ...
666s Selecting previously unselected package libglapi-mesa:amd64.
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666s Selecting previously unselected package libx11-xcb1:amd64.
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666s Selecting previously unselected package libxcb-dri2-0:amd64.
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666s Selecting previously unselected package libxcb-glx0:amd64.
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666s Selecting previously unselected package libxcb-randr0:amd64.
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666s Selecting previously unselected package libxcb-sync1:amd64.
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666s Selecting previously unselected package libxcb-xfixes0:amd64.
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666s Selecting previously unselected package libxshmfence1:amd64.
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666s Selecting previously unselected package libxxf86vm1:amd64.
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666s Selecting previously unselected package libdrm-amdgpu1:amd64.
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666s Selecting previously unselected package libpciaccess0:amd64.
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666s Selecting previously unselected package libdrm-intel1:amd64.
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666s Selecting previously unselected package libdrm-radeon1:amd64.
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666s Selecting previously unselected package mesa-libgallium:amd64.
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666s Selecting previously unselected package libvulkan1:amd64.
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666s Selecting previously unselected package libwayland-server0:amd64.
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666s Selecting previously unselected package libgbm1:amd64.
666s Preparing to unpack .../090-libgbm1_24.2.3-1ubuntu1_amd64.deb ...
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666s Selecting previously unselected package libgl1-mesa-dri:amd64.
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666s Selecting previously unselected package libglx-mesa0:amd64.
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666s Selecting previously unselected package libglx0:amd64.
666s Preparing to unpack .../093-libglx0_1.7.0-1build1_amd64.deb ...
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666s Selecting previously unselected package libgl1:amd64.
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666s Selecting previously unselected package libasound2-data.
667s Preparing to unpack .../095-libasound2-data_1.2.12-1_all.deb ...
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667s Selecting previously unselected package libasound2t64:amd64.
667s Preparing to unpack .../096-libasound2t64_1.2.12-1_amd64.deb ...
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667s Selecting previously unselected package libgif7:amd64.
667s Preparing to unpack .../097-libgif7_5.2.2-1ubuntu1_amd64.deb ...
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667s Selecting previously unselected package x11-common.
667s Preparing to unpack .../098-x11-common_1%3a7.7+23ubuntu3_all.deb ...
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667s Selecting previously unselected package libxtst6:amd64.
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667s Unpacking libxtst6:amd64 (2:1.2.3-1.1build1) ...
667s Selecting previously unselected package openjdk-21-jre:amd64.
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667s Selecting previously unselected package fonts-font-awesome.
667s Preparing to unpack .../102-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ...
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667s Selecting previously unselected package fonts-glyphicons-halflings.
667s Preparing to unpack .../103-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ...
667s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ...
667s Selecting previously unselected package fonts-lmodern.
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667s Unpacking fonts-lmodern (2.005-1) ...
667s Selecting previously unselected package fonts-mathjax.
667s Preparing to unpack .../105-fonts-mathjax_2.7.9+dfsg-1_all.deb ...
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667s Selecting previously unselected package hisat2.
667s Preparing to unpack .../106-hisat2_2.2.1-5_amd64.deb ...
667s Unpacking hisat2 (2.2.1-5) ...
667s Selecting previously unselected package jaligner.
667s Preparing to unpack .../107-jaligner_1.0+dfsg-11_all.deb ...
667s Unpacking jaligner (1.0+dfsg-11) ...
667s Selecting previously unselected package javascript-common.
667s Preparing to unpack .../108-javascript-common_11+nmu1_all.deb ...
667s Unpacking javascript-common (11+nmu1) ...
667s Selecting previously unselected package libhtscodecs2:amd64.
667s Preparing to unpack .../109-libhtscodecs2_1.6.0-1build1_amd64.deb ...
667s Unpacking libhtscodecs2:amd64 (1.6.0-1build1) ...
667s Selecting previously unselected package libhts3t64:amd64.
667s Preparing to unpack .../110-libhts3t64_1.20+ds-2_amd64.deb ...
667s Unpacking libhts3t64:amd64 (1.20+ds-2) ...
667s Selecting previously unselected package libjellyfish-2.0-2:amd64.
667s Preparing to unpack .../111-libjellyfish-2.0-2_2.3.1-3build2_amd64.deb ...
667s Unpacking libjellyfish-2.0-2:amd64 (2.3.1-3build2) ...
667s Selecting previously unselected package jellyfish.
667s Preparing to unpack .../112-jellyfish_2.3.1-3build2_amd64.deb ...
667s Unpacking jellyfish (2.3.1-3build2) ...
667s Selecting previously unselected package kallisto.
667s Preparing to unpack .../113-kallisto_0.48.0+dfsg-4build1_amd64.deb ...
667s Unpacking kallisto (0.48.0+dfsg-4build1) ...
668s Selecting previously unselected package libapache-pom-java.
668s Preparing to unpack .../114-libapache-pom-java_33-2_all.deb ...
668s Unpacking libapache-pom-java (33-2) ...
668s Selecting previously unselected package libasan8:amd64.
668s Preparing to unpack .../115-libasan8_14.2.0-7ubuntu1_amd64.deb ...
668s Unpacking libasan8:amd64 (14.2.0-7ubuntu1) ...
668s Selecting previously unselected package libatinject-jsr330-api-java.
668s Preparing to unpack .../116-libatinject-jsr330-api-java_1.0+ds1-5_all.deb ...
668s Unpacking libatinject-jsr330-api-java (1.0+ds1-5) ...
668s Selecting previously unselected package libcommons-parent-java.
668s Preparing to unpack .../117-libcommons-parent-java_56-1_all.deb ...
668s Unpacking libcommons-parent-java (56-1) ...
668s Selecting previously unselected package libcommons-lang3-java.
668s Preparing to unpack .../118-libcommons-lang3-java_3.14.0-1_all.deb ...
668s Unpacking libcommons-lang3-java (3.14.0-1) ...
668s Selecting previously unselected package libfreemarker-java.
668s Preparing to unpack .../119-libfreemarker-java_2.3.32-2_all.deb ...
668s Unpacking libfreemarker-java (2.3.32-2) ...
668s Selecting previously unselected package libgoogle-gson-java.
668s Preparing to unpack .../120-libgoogle-gson-java_2.10.1-1_all.deb ...
668s Unpacking libgoogle-gson-java (2.10.1-1) ...
668s Selecting previously unselected package libjoptsimple-java.
668s Preparing to unpack .../121-libjoptsimple-java_5.0.4-4_all.deb ...
668s Unpacking libjoptsimple-java (5.0.4-4) ...
668s Selecting previously unselected package libcommons-codec-java.
668s Preparing to unpack .../122-libcommons-codec-java_1.16.0-1_all.deb ...
668s Unpacking libcommons-codec-java (1.16.0-1) ...
668s Selecting previously unselected package libcommons-logging-java.
668s Preparing to unpack .../123-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ...
668s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ...
668s Selecting previously unselected package libhttpcore-java.
668s Preparing to unpack .../124-libhttpcore-java_4.4.16-1_all.deb ...
668s Unpacking libhttpcore-java (4.4.16-1) ...
668s Selecting previously unselected package libhttpclient-java.
668s Preparing to unpack .../125-libhttpclient-java_4.5.14-1_all.deb ...
668s Unpacking libhttpclient-java (4.5.14-1) ...
668s Selecting previously unselected package liblightcouch-java.
668s Preparing to unpack .../126-liblightcouch-java_0.2.0-1_all.deb ...
668s Unpacking liblightcouch-java (0.2.0-1) ...
668s Selecting previously unselected package libmongodb-java.
668s Preparing to unpack .../127-libmongodb-java_3.6.3-2_all.deb ...
668s Unpacking libmongodb-java (3.6.3-2) ...
668s Selecting previously unselected package libslf4j-java.
668s Preparing to unpack .../128-libslf4j-java_1.7.32-1_all.deb ...
668s Unpacking libslf4j-java (1.7.32-1) ...
668s Selecting previously unselected package liblog4j2-java.
668s Preparing to unpack .../129-liblog4j2-java_2.19.0-2_all.deb ...
668s Unpacking liblog4j2-java (2.19.0-2) ...
668s Selecting previously unselected package libbarclay-java.
668s Preparing to unpack .../130-libbarclay-java_5.0.0+dfsg-1_all.deb ...
668s Unpacking libbarclay-java (5.0.0+dfsg-1) ...
668s Selecting previously unselected package libio-string-perl.
668s Preparing to unpack .../131-libio-string-perl_1.08-4_all.deb ...
668s Unpacking libio-string-perl (1.08-4) ...
668s Selecting previously unselected package liblatex-tounicode-perl.
668s Preparing to unpack .../132-liblatex-tounicode-perl_0.54-2_all.deb ...
668s Unpacking liblatex-tounicode-perl (0.54-2) ...
668s Selecting previously unselected package libbibtex-parser-perl.
668s Preparing to unpack .../133-libbibtex-parser-perl_1.04+dfsg-1_all.deb ...
668s Unpacking libbibtex-parser-perl (1.04+dfsg-1) ...
668s Selecting previously unselected package libblas3:amd64.
668s Preparing to unpack .../134-libblas3_3.12.0-3build2_amd64.deb ...
668s Unpacking libblas3:amd64 (3.12.0-3build2) ...
668s Selecting previously unselected package libgomp1:amd64.
668s Preparing to unpack .../135-libgomp1_14.2.0-7ubuntu1_amd64.deb ...
668s Unpacking libgomp1:amd64 (14.2.0-7ubuntu1) ...
668s Selecting previously unselected package libitm1:amd64.
669s Preparing to unpack .../136-libitm1_14.2.0-7ubuntu1_amd64.deb ...
669s Unpacking libitm1:amd64 (14.2.0-7ubuntu1) ...
669s Selecting previously unselected package liblsan0:amd64.
669s Preparing to unpack .../137-liblsan0_14.2.0-7ubuntu1_amd64.deb ...
669s Unpacking liblsan0:amd64 (14.2.0-7ubuntu1) ...
669s Selecting previously unselected package libtsan2:amd64.
669s Preparing to unpack .../138-libtsan2_14.2.0-7ubuntu1_amd64.deb ...
669s Unpacking libtsan2:amd64 (14.2.0-7ubuntu1) ...
669s Selecting previously unselected package libubsan1:amd64.
669s Preparing to unpack .../139-libubsan1_14.2.0-7ubuntu1_amd64.deb ...
669s Unpacking libubsan1:amd64 (14.2.0-7ubuntu1) ...
669s Selecting previously unselected package libhwasan0:amd64.
669s Preparing to unpack .../140-libhwasan0_14.2.0-7ubuntu1_amd64.deb ...
669s Unpacking libhwasan0:amd64 (14.2.0-7ubuntu1) ...
669s Selecting previously unselected package libquadmath0:amd64.
669s Preparing to unpack .../141-libquadmath0_14.2.0-7ubuntu1_amd64.deb ...
669s Unpacking libquadmath0:amd64 (14.2.0-7ubuntu1) ...
669s Selecting previously unselected package libgcc-14-dev:amd64.
669s Preparing to unpack .../142-libgcc-14-dev_14.2.0-7ubuntu1_amd64.deb ...
669s Unpacking libgcc-14-dev:amd64 (14.2.0-7ubuntu1) ...
669s Selecting previously unselected package libstdc++-14-dev:amd64.
669s Preparing to unpack .../143-libstdc++-14-dev_14.2.0-7ubuntu1_amd64.deb ...
669s Unpacking libstdc++-14-dev:amd64 (14.2.0-7ubuntu1) ...
669s Selecting previously unselected package libboost1.83-dev:amd64.
669s Preparing to unpack .../144-libboost1.83-dev_1.83.0-3.2ubuntu2_amd64.deb ...
669s Unpacking libboost1.83-dev:amd64 (1.83.0-3.2ubuntu2) ...
672s Selecting previously unselected package libboost-dev:amd64.
672s Preparing to unpack .../145-libboost-dev_1.83.0.2ubuntu1_amd64.deb ...
672s Unpacking libboost-dev:amd64 (1.83.0.2ubuntu1) ...
672s Selecting previously unselected package libboost-iostreams1.83.0:amd64.
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672s Unpacking libboost-iostreams1.83.0:amd64 (1.83.0-3.2ubuntu2) ...
672s Selecting previously unselected package libclone-perl:amd64.
672s Preparing to unpack .../147-libclone-perl_0.47-1_amd64.deb ...
672s Unpacking libclone-perl:amd64 (0.47-1) ...
672s Selecting previously unselected package libcommons-compress-java.
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672s Unpacking libcommons-compress-java (1.25.0-1) ...
672s Selecting previously unselected package libcommons-io-java.
672s Preparing to unpack .../149-libcommons-io-java_2.16.1-1_all.deb ...
672s Unpacking libcommons-io-java (2.16.1-1) ...
672s Selecting previously unselected package libcommons-jexl2-java.
672s Preparing to unpack .../150-libcommons-jexl2-java_2.1.1-6_all.deb ...
672s Unpacking libcommons-jexl2-java (2.1.1-6) ...
672s Selecting previously unselected package libcommons-math3-java.
672s Preparing to unpack .../151-libcommons-math3-java_3.6.1-3_all.deb ...
672s Unpacking libcommons-math3-java (3.6.1-3) ...
672s Selecting previously unselected package libencode-locale-perl.
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672s Unpacking libencode-locale-perl (1.05-3) ...
672s Selecting previously unselected package libjsr305-java.
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672s Unpacking libjsr305-java (0.1~+svn49-11) ...
672s Selecting previously unselected package libguava-java.
672s Preparing to unpack .../154-libguava-java_32.0.1-1_all.deb ...
672s Unpacking libguava-java (32.0.1-1) ...
672s Selecting previously unselected package liberror-prone-java.
672s Preparing to unpack .../155-liberror-prone-java_2.18.0-1_all.deb ...
672s Unpacking liberror-prone-java (2.18.0-1) ...
672s Selecting previously unselected package libtimedate-perl.
672s Preparing to unpack .../156-libtimedate-perl_2.3300-2_all.deb ...
672s Unpacking libtimedate-perl (2.3300-2) ...
672s Selecting previously unselected package libhttp-date-perl.
672s Preparing to unpack .../157-libhttp-date-perl_6.06-1_all.deb ...
672s Unpacking libhttp-date-perl (6.06-1) ...
672s Selecting previously unselected package libfile-listing-perl.
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672s Unpacking libfile-listing-perl (6.16-1) ...
672s Selecting previously unselected package libgatk-native-bindings-java.
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672s Unpacking libgatk-native-bindings-java (1.0.0+dfsg-2) ...
672s Selecting previously unselected package libgetopt-java.
672s Preparing to unpack .../160-libgetopt-java_1.0.14+dfsg-6_all.deb ...
672s Unpacking libgetopt-java (1.0.14+dfsg-6) ...
672s Selecting previously unselected package libgfortran5:amd64.
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672s Unpacking libgfortran5:amd64 (14.2.0-7ubuntu1) ...
672s Selecting previously unselected package libmjson-java.
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672s Unpacking libmjson-java (1.4.0-3) ...
672s Selecting previously unselected package libmbedcrypto7t64:amd64.
672s Preparing to unpack .../163-libmbedcrypto7t64_2.28.8-1_amd64.deb ...
672s Unpacking libmbedcrypto7t64:amd64 (2.28.8-1) ...
672s Selecting previously unselected package libmbedx509-1t64:amd64.
672s Preparing to unpack .../164-libmbedx509-1t64_2.28.8-1_amd64.deb ...
672s Unpacking libmbedx509-1t64:amd64 (2.28.8-1) ...
672s Selecting previously unselected package libmbedtls14t64:amd64.
672s Preparing to unpack .../165-libmbedtls14t64_2.28.8-1_amd64.deb ...
672s Unpacking libmbedtls14t64:amd64 (2.28.8-1) ...
672s Selecting previously unselected package ncbi-vdb-data.
673s Preparing to unpack .../166-ncbi-vdb-data_3.0.2+dfsg-2build2_all.deb ...
673s Unpacking ncbi-vdb-data (3.0.2+dfsg-2build2) ...
673s Selecting previously unselected package libncbi-vdb3:amd64.
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673s Unpacking libncbi-vdb3:amd64 (3.0.2+dfsg-2build2) ...
673s Selecting previously unselected package libncbi-ngs3:amd64.
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673s Unpacking libncbi-ngs3:amd64 (3.0.3+dfsg-9ubuntu1) ...
673s Selecting previously unselected package libngs-jni:amd64.
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673s Unpacking libngs-jni:amd64 (3.0.3+dfsg-9ubuntu1) ...
673s Selecting previously unselected package libngs-java:amd64.
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673s Unpacking libngs-java:amd64 (3.0.3+dfsg-9ubuntu1) ...
673s Selecting previously unselected package librhino-java.
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673s Selecting previously unselected package libsnappy1v5:amd64.
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673s Selecting previously unselected package libsnappy-jni.
673s Preparing to unpack .../173-libsnappy-jni_1.1.10.5-2_amd64.deb ...
673s Unpacking libsnappy-jni (1.1.10.5-2) ...
673s Selecting previously unselected package libsnappy-java.
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673s Selecting previously unselected package libhtsjdk-java.
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673s Selecting previously unselected package libgkl-java.
673s Preparing to unpack .../176-libgkl-java_0.8.11+dfsg-2build1_all.deb ...
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673s Selecting previously unselected package libhtml-tagset-perl.
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673s Selecting previously unselected package liburi-perl.
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673s Selecting previously unselected package libhtml-parser-perl:amd64.
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673s Selecting previously unselected package libhtml-tree-perl.
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673s Selecting previously unselected package libio-html-perl.
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673s Selecting previously unselected package liblwp-mediatypes-perl.
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673s Selecting previously unselected package libhttp-cookies-perl.
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673s Selecting previously unselected package libhwloc15:amd64.
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673s Selecting previously unselected package libnet-ssleay-perl:amd64.
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673s Selecting previously unselected package libio-socket-ssl-perl.
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674s Selecting previously unselected package libjs-bootstrap.
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674s Selecting previously unselected package libjs-popper.js.
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674s Selecting previously unselected package libjs-jquery-ui.
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674s Selecting previously unselected package libjs-json.
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674s Selecting previously unselected package libjs-underscore.
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674s Selecting previously unselected package libjs-sphinxdoc.
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674s Selecting previously unselected package libjung-free-java.
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674s Selecting previously unselected package libkpathsea6:amd64.
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674s Selecting previously unselected package liblapack3:amd64.
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674s Selecting previously unselected package liblua5.4-0:amd64.
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675s Selecting previously unselected package libnet-http-perl.
675s Preparing to unpack .../213-libnet-http-perl_6.23-1_all.deb ...
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675s Selecting previously unselected package libtry-tiny-perl.
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675s Selecting previously unselected package libwww-robotrules-perl.
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675s Selecting previously unselected package libwww-perl.
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675s Selecting previously unselected package liblwp-protocol-https-perl.
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675s Selecting previously unselected package libmpfi0:amd64.
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675s Selecting previously unselected package libpaper1:amd64.
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675s Selecting previously unselected package libpaper-utils.
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675s Selecting previously unselected package libpicard-java.
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675s Selecting previously unselected package libpotrace0:amd64.
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675s Selecting previously unselected package libptexenc1:amd64.
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675s Selecting previously unselected package libsm6:amd64.
675s Preparing to unpack .../224-libsm6_2%3a1.2.3-1build3_amd64.deb ...
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675s Selecting previously unselected package libstaden-read14t64:amd64.
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675s Selecting previously unselected package libsynctex2:amd64.
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675s Selecting previously unselected package libtbbmalloc2:amd64.
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675s Selecting previously unselected package libtbbbind-2-5:amd64.
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675s Selecting previously unselected package libtbb12:amd64.
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675s Selecting previously unselected package libtcl8.6:amd64.
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675s Selecting previously unselected package libteckit0:amd64.
675s Preparing to unpack .../231-libteckit0_2.5.12+ds1-1_amd64.deb ...
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675s Selecting previously unselected package libtexlua53-5:amd64.
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675s Selecting previously unselected package libxft2:amd64.
675s Preparing to unpack .../233-libxft2_2.3.6-1build1_amd64.deb ...
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675s Selecting previously unselected package libxss1:amd64.
675s Preparing to unpack .../234-libxss1_1%3a1.2.3-1build3_amd64.deb ...
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675s Selecting previously unselected package libtk8.6:amd64.
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675s Selecting previously unselected package libxt6t64:amd64.
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676s Selecting previously unselected package libxmu6:amd64.
676s Preparing to unpack .../237-libxmu6_2%3a1.1.3-3build2_amd64.deb ...
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676s Selecting previously unselected package libxpm4:amd64.
676s Preparing to unpack .../238-libxpm4_1%3a3.5.17-1build2_amd64.deb ...
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676s Selecting previously unselected package libxaw7:amd64.
676s Preparing to unpack .../239-libxaw7_2%3a1.0.14-1build2_amd64.deb ...
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676s Selecting previously unselected package libzzip-0-13t64:amd64.
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676s Selecting previously unselected package zip.
676s Preparing to unpack .../241-zip_3.0-14_amd64.deb ...
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676s Preparing to unpack .../242-unzip_6.0-28ubuntu6_amd64.deb ...
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676s Selecting previously unselected package xdg-utils.
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676s Selecting previously unselected package r-base-core.
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676s Selecting previously unselected package r-cran-littler.
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676s Selecting previously unselected package littler.
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676s Selecting previously unselected package ncbi-data.
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676s Selecting previously unselected package ncbi-blast+.
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677s Selecting previously unselected package node-bootstrap-sass.
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677s Selecting previously unselected package node-html5shiv.
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677s Selecting previously unselected package node-normalize.css.
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677s Selecting previously unselected package pandoc-data.
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677s Selecting previously unselected package pandoc.
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677s Unpacking pandoc (3.1.11.1+ds-2) ...
678s Selecting previously unselected package parafly.
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678s Selecting previously unselected package python3-hisat2.
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678s Selecting previously unselected package python3-numpy.
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678s Unpacking python3-numpy (1:1.26.4+ds-11build1) ...
678s Selecting previously unselected package python3-pysam.
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678s Selecting previously unselected package python3-htseq.
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678s Selecting previously unselected package r-bioc-biocgenerics.
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678s Selecting previously unselected package r-bioc-biobase.
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678s Selecting previously unselected package r-bioc-s4vectors.
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678s Selecting previously unselected package r-bioc-iranges.
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678s Selecting previously unselected package r-cran-dbi.
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678s Selecting previously unselected package r-cran-bit.
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679s Selecting previously unselected package r-cran-bit64.
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679s Selecting previously unselected package r-cran-rlang.
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679s Selecting previously unselected package r-cran-cli.
679s Preparing to unpack .../267-r-cran-cli_3.6.2-1_amd64.deb ...
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679s Selecting previously unselected package r-cran-glue.
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679s Selecting previously unselected package r-cran-lifecycle.
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679s Selecting previously unselected package r-cran-vctrs.
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679s Selecting previously unselected package r-cran-blob.
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679s Selecting previously unselected package r-cran-fastmap.
679s Preparing to unpack .../272-r-cran-fastmap_1.1.1-1_amd64.deb ...
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679s Selecting previously unselected package r-cran-cachem.
679s Preparing to unpack .../273-r-cran-cachem_1.0.8-1_amd64.deb ...
679s Unpacking r-cran-cachem (1.0.8-1) ...
679s Selecting previously unselected package r-cran-memoise.
679s Preparing to unpack .../274-r-cran-memoise_2.0.1-1_all.deb ...
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679s Selecting previously unselected package r-cran-pkgconfig.
679s Preparing to unpack .../275-r-cran-pkgconfig_2.0.3-2build1_all.deb ...
679s Unpacking r-cran-pkgconfig (2.0.3-2build1) ...
679s Selecting previously unselected package r-cran-plogr.
679s Preparing to unpack .../276-r-cran-plogr_0.2.0-3build1_all.deb ...
679s Unpacking r-cran-plogr (0.2.0-3build1) ...
679s Selecting previously unselected package r-cran-cpp11.
679s Preparing to unpack .../277-r-cran-cpp11_0.4.7-1_all.deb ...
679s Unpacking r-cran-cpp11 (0.4.7-1) ...
679s Selecting previously unselected package r-cran-rsqlite.
679s Preparing to unpack .../278-r-cran-rsqlite_2.3.7-2_amd64.deb ...
679s Unpacking r-cran-rsqlite (2.3.7-2) ...
679s Selecting previously unselected package r-cran-curl.
679s Preparing to unpack .../279-r-cran-curl_5.2.1+dfsg-1_amd64.deb ...
679s Unpacking r-cran-curl (5.2.1+dfsg-1) ...
679s Selecting previously unselected package r-cran-jsonlite.
679s Preparing to unpack .../280-r-cran-jsonlite_1.8.8+dfsg-1_amd64.deb ...
679s Unpacking r-cran-jsonlite (1.8.8+dfsg-1) ...
679s Selecting previously unselected package r-cran-mime.
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679s Unpacking r-cran-mime (0.12-2) ...
679s Selecting previously unselected package r-cran-sys.
679s Preparing to unpack .../282-r-cran-sys_3.4.2-1_amd64.deb ...
679s Unpacking r-cran-sys (3.4.2-1) ...
679s Selecting previously unselected package r-cran-askpass.
679s Preparing to unpack .../283-r-cran-askpass_1.2.0-1_amd64.deb ...
679s Unpacking r-cran-askpass (1.2.0-1) ...
679s Selecting previously unselected package r-cran-openssl.
679s Preparing to unpack .../284-r-cran-openssl_2.2.0+dfsg-1_amd64.deb ...
679s Unpacking r-cran-openssl (2.2.0+dfsg-1) ...
679s Selecting previously unselected package r-cran-r6.
679s Preparing to unpack .../285-r-cran-r6_2.5.1-1_all.deb ...
679s Unpacking r-cran-r6 (2.5.1-1) ...
679s Selecting previously unselected package r-cran-httr.
679s Preparing to unpack .../286-r-cran-httr_1.4.7+dfsg-1_all.deb ...
679s Unpacking r-cran-httr (1.4.7+dfsg-1) ...
680s Selecting previously unselected package r-cran-png.
680s Preparing to unpack .../287-r-cran-png_0.1-8-1build2_amd64.deb ...
680s Unpacking r-cran-png (0.1-8-1build2) ...
680s Selecting previously unselected package zlib1g-dev:amd64.
680s Preparing to unpack .../288-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ...
680s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
680s Selecting previously unselected package r-bioc-zlibbioc.
680s Preparing to unpack .../289-r-bioc-zlibbioc_1.50.0+dfsg-2_all.deb ...
680s Unpacking r-bioc-zlibbioc (1.50.0+dfsg-2) ...
680s Selecting previously unselected package r-bioc-xvector.
680s Preparing to unpack .../290-r-bioc-xvector_0.44.0-1_amd64.deb ...
680s Unpacking r-bioc-xvector (0.44.0-1) ...
680s Selecting previously unselected package r-bioc-ucsc.utils.
680s Preparing to unpack .../291-r-bioc-ucsc.utils_1.0.0+ds-2_all.deb ...
680s Unpacking r-bioc-ucsc.utils (1.0.0+ds-2) ...
680s Selecting previously unselected package r-bioc-genomeinfodbdata.
680s Preparing to unpack .../292-r-bioc-genomeinfodbdata_1.2.12-1_all.deb ...
680s Unpacking r-bioc-genomeinfodbdata (1.2.12-1) ...
680s Selecting previously unselected package r-bioc-genomeinfodb.
680s Preparing to unpack .../293-r-bioc-genomeinfodb_1.40.1+dfsg-1_all.deb ...
680s Unpacking r-bioc-genomeinfodb (1.40.1+dfsg-1) ...
680s Selecting previously unselected package r-cran-crayon.
680s Preparing to unpack .../294-r-cran-crayon_1.5.2-1_all.deb ...
680s Unpacking r-cran-crayon (1.5.2-1) ...
680s Selecting previously unselected package r-bioc-biostrings.
680s Preparing to unpack .../295-r-bioc-biostrings_2.72.1+dfsg-1_amd64.deb ...
680s Unpacking r-bioc-biostrings (2.72.1+dfsg-1) ...
680s Selecting previously unselected package r-bioc-keggrest.
680s Preparing to unpack .../296-r-bioc-keggrest_1.44.1+dfsg-1_all.deb ...
680s Unpacking r-bioc-keggrest (1.44.1+dfsg-1) ...
680s Selecting previously unselected package r-bioc-annotationdbi.
680s Preparing to unpack .../297-r-bioc-annotationdbi_1.66.0-1_all.deb ...
680s Unpacking r-bioc-annotationdbi (1.66.0-1) ...
680s Selecting previously unselected package r-cran-xml.
680s Preparing to unpack .../298-r-cran-xml_3.99-0.17-1_amd64.deb ...
680s Unpacking r-cran-xml (3.99-0.17-1) ...
680s Selecting previously unselected package r-cran-xtable.
680s Preparing to unpack .../299-r-cran-xtable_1%3a1.8-4-2_all.deb ...
680s Unpacking r-cran-xtable (1:1.8-4-2) ...
680s Selecting previously unselected package r-bioc-annotate.
680s Preparing to unpack .../300-r-bioc-annotate_1.82.0+dfsg-1_all.deb ...
680s Unpacking r-bioc-annotate (1.82.0+dfsg-1) ...
680s Selecting previously unselected package r-cran-generics.
680s Preparing to unpack .../301-r-cran-generics_0.1.3-1_all.deb ...
680s Unpacking r-cran-generics (0.1.3-1) ...
680s Selecting previously unselected package r-cran-magrittr.
680s Preparing to unpack .../302-r-cran-magrittr_2.0.3-1_amd64.deb ...
680s Unpacking r-cran-magrittr (2.0.3-1) ...
680s Selecting previously unselected package r-cran-fansi.
680s Preparing to unpack .../303-r-cran-fansi_1.0.5-1_amd64.deb ...
680s Unpacking r-cran-fansi (1.0.5-1) ...
680s Selecting previously unselected package r-cran-utf8.
680s Preparing to unpack .../304-r-cran-utf8_1.2.4-1_amd64.deb ...
680s Unpacking r-cran-utf8 (1.2.4-1) ...
681s Selecting previously unselected package r-cran-pillar.
681s Preparing to unpack .../305-r-cran-pillar_1.9.0+dfsg-1_all.deb ...
681s Unpacking r-cran-pillar (1.9.0+dfsg-1) ...
681s Selecting previously unselected package r-cran-tibble.
681s Preparing to unpack .../306-r-cran-tibble_3.2.1+dfsg-2_amd64.deb ...
681s Unpacking r-cran-tibble (3.2.1+dfsg-2) ...
681s Selecting previously unselected package r-cran-withr.
681s Preparing to unpack .../307-r-cran-withr_3.0.0+dfsg-1_all.deb ...
681s Unpacking r-cran-withr (3.0.0+dfsg-1) ...
681s Selecting previously unselected package r-cran-tidyselect.
681s Preparing to unpack .../308-r-cran-tidyselect_1.2.1+dfsg-1_amd64.deb ...
681s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ...
681s Selecting previously unselected package r-cran-dplyr.
681s Preparing to unpack .../309-r-cran-dplyr_1.1.4-1_amd64.deb ...
681s Unpacking r-cran-dplyr (1.1.4-1) ...
681s Selecting previously unselected package r-cran-purrr.
681s Preparing to unpack .../310-r-cran-purrr_1.0.2-1_amd64.deb ...
681s Unpacking r-cran-purrr (1.0.2-1) ...
681s Selecting previously unselected package r-cran-stringi.
681s Preparing to unpack .../311-r-cran-stringi_1.8.3-1_amd64.deb ...
681s Unpacking r-cran-stringi (1.8.3-1) ...
681s Selecting previously unselected package r-cran-stringr.
681s Preparing to unpack .../312-r-cran-stringr_1.5.1-1_all.deb ...
681s Unpacking r-cran-stringr (1.5.1-1) ...
681s Selecting previously unselected package r-cran-tidyr.
681s Preparing to unpack .../313-r-cran-tidyr_1.3.1-1_amd64.deb ...
681s Unpacking r-cran-tidyr (1.3.1-1) ...
681s Selecting previously unselected package r-cran-dbplyr.
681s Preparing to unpack .../314-r-cran-dbplyr_2.4.0+dfsg-1_all.deb ...
681s Unpacking r-cran-dbplyr (2.4.0+dfsg-1) ...
681s Selecting previously unselected package r-cran-filelock.
681s Preparing to unpack .../315-r-cran-filelock_1.0.3-1_amd64.deb ...
681s Unpacking r-cran-filelock (1.0.3-1) ...
681s Selecting previously unselected package r-bioc-biocfilecache.
681s Preparing to unpack .../316-r-bioc-biocfilecache_2.12.0+dfsg-1_all.deb ...
681s Unpacking r-bioc-biocfilecache (2.12.0+dfsg-1) ...
681s Selecting previously unselected package r-bioc-biocio.
681s Preparing to unpack .../317-r-bioc-biocio_1.14.0+dfsg-1_all.deb ...
681s Unpacking r-bioc-biocio (1.14.0+dfsg-1) ...
681s Selecting previously unselected package r-cran-formatr.
681s Preparing to unpack .../318-r-cran-formatr_1.14-2_all.deb ...
681s Unpacking r-cran-formatr (1.14-2) ...
681s Selecting previously unselected package r-cran-lambda.r.
681s Preparing to unpack .../319-r-cran-lambda.r_1.2.4-2build1_all.deb ...
681s Unpacking r-cran-lambda.r (1.2.4-2build1) ...
681s Selecting previously unselected package r-cran-futile.options.
681s Preparing to unpack .../320-r-cran-futile.options_1.0.1-3build1_all.deb ...
681s Unpacking r-cran-futile.options (1.0.1-3build1) ...
681s Selecting previously unselected package r-cran-futile.logger.
681s Preparing to unpack .../321-r-cran-futile.logger_1.4.3-4build1_all.deb ...
681s Unpacking r-cran-futile.logger (1.4.3-4build1) ...
681s Selecting previously unselected package r-cran-snow.
681s Preparing to unpack .../322-r-cran-snow_1%3a0.4.4-2_all.deb ...
681s Unpacking r-cran-snow (1:0.4.4-2) ...
681s Selecting previously unselected package r-cran-codetools.
681s Preparing to unpack .../323-r-cran-codetools_0.2-20-1_all.deb ...
681s Unpacking r-cran-codetools (0.2-20-1) ...
681s Selecting previously unselected package r-cran-bh.
681s Preparing to unpack .../324-r-cran-bh_1.84.0-1_all.deb ...
681s Unpacking r-cran-bh (1.84.0-1) ...
681s Selecting previously unselected package r-bioc-biocparallel.
681s Preparing to unpack .../325-r-bioc-biocparallel_1.38.0-2_amd64.deb ...
681s Unpacking r-bioc-biocparallel (1.38.0-2) ...
681s Selecting previously unselected package r-cran-base64enc.
682s Preparing to unpack .../326-r-cran-base64enc_0.1-3-3_amd64.deb ...
682s Unpacking r-cran-base64enc (0.1-3-3) ...
682s Selecting previously unselected package r-cran-digest.
682s Preparing to unpack .../327-r-cran-digest_0.6.36-1_amd64.deb ...
682s Unpacking r-cran-digest (0.6.36-1) ...
682s Selecting previously unselected package r-cran-htmltools.
682s Preparing to unpack .../328-r-cran-htmltools_0.5.8.1-1_amd64.deb ...
682s Unpacking r-cran-htmltools (0.5.8.1-1) ...
682s Selecting previously unselected package r-cran-evaluate.
682s Preparing to unpack .../329-r-cran-evaluate_0.24.0-1_all.deb ...
682s Unpacking r-cran-evaluate (0.24.0-1) ...
682s Selecting previously unselected package r-cran-xfun.
682s Preparing to unpack .../330-r-cran-xfun_0.45+dfsg-1_amd64.deb ...
682s Unpacking r-cran-xfun (0.45+dfsg-1) ...
682s Selecting previously unselected package r-cran-highr.
682s Preparing to unpack .../331-r-cran-highr_0.11+dfsg-1_all.deb ...
682s Unpacking r-cran-highr (0.11+dfsg-1) ...
682s Selecting previously unselected package r-cran-yaml.
682s Preparing to unpack .../332-r-cran-yaml_2.3.8-2_amd64.deb ...
682s Unpacking r-cran-yaml (2.3.8-2) ...
682s Selecting previously unselected package libjs-mathjax.
682s Preparing to unpack .../333-libjs-mathjax_2.7.9+dfsg-1_all.deb ...
682s Unpacking libjs-mathjax (2.7.9+dfsg-1) ...
683s Selecting previously unselected package r-cran-knitr.
683s Preparing to unpack .../334-r-cran-knitr_1.47+dfsg-1_all.deb ...
683s Unpacking r-cran-knitr (1.47+dfsg-1) ...
683s Selecting previously unselected package r-cran-jquerylib.
683s Preparing to unpack .../335-r-cran-jquerylib_0.1.4+dfsg-4_all.deb ...
683s Unpacking r-cran-jquerylib (0.1.4+dfsg-4) ...
683s Selecting previously unselected package r-cran-fs.
683s Preparing to unpack .../336-r-cran-fs_1.6.4+dfsg-1_amd64.deb ...
683s Unpacking r-cran-fs (1.6.4+dfsg-1) ...
683s Selecting previously unselected package r-cran-rappdirs.
683s Preparing to unpack .../337-r-cran-rappdirs_0.3.3-1_amd64.deb ...
683s Unpacking r-cran-rappdirs (0.3.3-1) ...
683s Selecting previously unselected package r-cran-sass.
683s Preparing to unpack .../338-r-cran-sass_0.4.9+dfsg-1_amd64.deb ...
683s Unpacking r-cran-sass (0.4.9+dfsg-1) ...
683s Selecting previously unselected package r-cran-bslib.
683s Preparing to unpack .../339-r-cran-bslib_0.7.0+dfsg-1_all.deb ...
683s Unpacking r-cran-bslib (0.7.0+dfsg-1) ...
683s Selecting previously unselected package r-cran-fontawesome.
683s Preparing to unpack .../340-r-cran-fontawesome_0.5.2-1_all.deb ...
683s Unpacking r-cran-fontawesome (0.5.2-1) ...
683s Selecting previously unselected package r-cran-tinytex.
683s Preparing to unpack .../341-r-cran-tinytex_0.51-1_all.deb ...
683s Unpacking r-cran-tinytex (0.51-1) ...
683s Selecting previously unselected package libjs-modernizr.
683s Preparing to unpack .../342-libjs-modernizr_3.13.0-0.1_all.deb ...
683s Unpacking libjs-modernizr (3.13.0-0.1) ...
683s Selecting previously unselected package r-cran-pkgkitten.
683s Preparing to unpack .../343-r-cran-pkgkitten_0.2.4-1_all.deb ...
683s Unpacking r-cran-pkgkitten (0.2.4-1) ...
683s Selecting previously unselected package r-cran-rcpp.
683s Preparing to unpack .../344-r-cran-rcpp_1.0.13-1_amd64.deb ...
683s Unpacking r-cran-rcpp (1.0.13-1) ...
683s Selecting previously unselected package r-cran-later.
683s Preparing to unpack .../345-r-cran-later_1.3.2+dfsg-1_amd64.deb ...
683s Unpacking r-cran-later (1.3.2+dfsg-1) ...
683s Selecting previously unselected package r-cran-promises.
683s Preparing to unpack .../346-r-cran-promises_1.3.0+dfsg-1_amd64.deb ...
683s Unpacking r-cran-promises (1.3.0+dfsg-1) ...
683s Selecting previously unselected package r-cran-httpuv.
683s Preparing to unpack .../347-r-cran-httpuv_1.6.15+dfsg-1_amd64.deb ...
683s Unpacking r-cran-httpuv (1.6.15+dfsg-1) ...
683s Selecting previously unselected package r-cran-sourcetools.
683s Preparing to unpack .../348-r-cran-sourcetools_0.1.7-1-1_amd64.deb ...
683s Unpacking r-cran-sourcetools (0.1.7-1-1) ...
684s Selecting previously unselected package r-cran-commonmark.
684s Preparing to unpack .../349-r-cran-commonmark_1.9.1-1_amd64.deb ...
684s Unpacking r-cran-commonmark (1.9.1-1) ...
684s Selecting previously unselected package libjs-twitter-bootstrap-datepicker.
684s Preparing to unpack .../350-libjs-twitter-bootstrap-datepicker_1.3.1+dfsg1-4.1_all.deb ...
684s Unpacking libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ...
684s Selecting previously unselected package r-cran-shiny.
684s Preparing to unpack .../351-r-cran-shiny_1.8.1.1+dfsg-1_all.deb ...
684s Unpacking r-cran-shiny (1.8.1.1+dfsg-1) ...
684s Selecting previously unselected package r-cran-rmarkdown.
684s Preparing to unpack .../352-r-cran-rmarkdown_2.27+dfsg-1_all.deb ...
684s Unpacking r-cran-rmarkdown (2.27+dfsg-1) ...
684s Selecting previously unselected package r-cran-bookdown.
684s Preparing to unpack .../353-r-cran-bookdown_0.40+dfsg-1_all.deb ...
684s Unpacking r-cran-bookdown (0.40+dfsg-1) ...
684s Selecting previously unselected package r-cran-biocmanager.
684s Preparing to unpack .../354-r-cran-biocmanager_1.30.22+dfsg-2_all.deb ...
684s Unpacking r-cran-biocmanager (1.30.22+dfsg-2) ...
684s Selecting previously unselected package tex-common.
684s Preparing to unpack .../355-tex-common_6.18_all.deb ...
684s Unpacking tex-common (6.18) ...
684s Selecting previously unselected package t1utils.
684s Preparing to unpack .../356-t1utils_1.41-4build3_amd64.deb ...
684s Unpacking t1utils (1.41-4build3) ...
684s Selecting previously unselected package texlive-binaries.
684s Preparing to unpack .../357-texlive-binaries_2024.20240313.70630+ds-4_amd64.deb ...
684s Unpacking texlive-binaries (2024.20240313.70630+ds-4) ...
684s Selecting previously unselected package texlive-base.
684s Preparing to unpack .../358-texlive-base_2024.20240706-1_all.deb ...
684s Unpacking texlive-base (2024.20240706-1) ...
685s Selecting previously unselected package texlive-latex-base.
685s Preparing to unpack .../359-texlive-latex-base_2024.20240706-1_all.deb ...
685s Unpacking texlive-latex-base (2024.20240706-1) ...
685s Selecting previously unselected package texlive-bibtex-extra.
685s Preparing to unpack .../360-texlive-bibtex-extra_2024.20240706-2_all.deb ...
685s Unpacking texlive-bibtex-extra (2024.20240706-2) ...
687s Selecting previously unselected package r-bioc-biocversion.
687s Preparing to unpack .../361-r-bioc-biocversion_3.19.1-1_all.deb ...
687s Unpacking r-bioc-biocversion (3.19.1-1) ...
687s Selecting previously unselected package r-bioc-biocstyle.
687s Preparing to unpack .../362-r-bioc-biocstyle_2.32.1+dfsg-1_all.deb ...
687s Unpacking r-bioc-biocstyle (2.32.1+dfsg-1) ...
688s Selecting previously unselected package r-cran-hms.
688s Preparing to unpack .../363-r-cran-hms_1.1.3-1_all.deb ...
688s Unpacking r-cran-hms (1.1.3-1) ...
688s Selecting previously unselected package r-cran-prettyunits.
688s Preparing to unpack .../364-r-cran-prettyunits_1.2.0-1_all.deb ...
688s Unpacking r-cran-prettyunits (1.2.0-1) ...
688s Selecting previously unselected package r-cran-progress.
688s Preparing to unpack .../365-r-cran-progress_1.2.3-1_all.deb ...
688s Unpacking r-cran-progress (1.2.3-1) ...
688s Selecting previously unselected package r-cran-httr2.
688s Preparing to unpack .../366-r-cran-httr2_1.0.2-1_all.deb ...
688s Unpacking r-cran-httr2 (1.0.2-1) ...
688s Selecting previously unselected package r-cran-xml2.
688s Preparing to unpack .../367-r-cran-xml2_1.3.6-1_amd64.deb ...
688s Unpacking r-cran-xml2 (1.3.6-1) ...
688s Selecting previously unselected package r-bioc-biomart.
688s Preparing to unpack .../368-r-bioc-biomart_2.60.1+dfsg-1_all.deb ...
688s Unpacking r-bioc-biomart (2.60.1+dfsg-1) ...
688s Selecting previously unselected package r-cran-lattice.
688s Preparing to unpack .../369-r-cran-lattice_0.22-6-1_amd64.deb ...
688s Unpacking r-cran-lattice (0.22-6-1) ...
688s Selecting previously unselected package r-cran-matrix.
688s Preparing to unpack .../370-r-cran-matrix_1.7-0-3_amd64.deb ...
688s Unpacking r-cran-matrix (1.7-0-3) ...
688s Selecting previously unselected package r-cran-matrixstats.
688s Preparing to unpack .../371-r-cran-matrixstats_1.3.0-1_amd64.deb ...
688s Unpacking r-cran-matrixstats (1.3.0-1) ...
688s Selecting previously unselected package r-bioc-matrixgenerics.
688s Preparing to unpack .../372-r-bioc-matrixgenerics_1.16.0-2_all.deb ...
688s Unpacking r-bioc-matrixgenerics (1.16.0-2) ...
688s Selecting previously unselected package r-cran-abind.
688s Preparing to unpack .../373-r-cran-abind_1.4-5-2_all.deb ...
688s Unpacking r-cran-abind (1.4-5-2) ...
688s Selecting previously unselected package r-bioc-s4arrays.
688s Preparing to unpack .../374-r-bioc-s4arrays_1.4.1+dfsg-1_amd64.deb ...
688s Unpacking r-bioc-s4arrays (1.4.1+dfsg-1) ...
688s Selecting previously unselected package r-bioc-sparsearray.
688s Preparing to unpack .../375-r-bioc-sparsearray_1.4.8+dfsg-1_amd64.deb ...
688s Unpacking r-bioc-sparsearray (1.4.8+dfsg-1) ...
688s Selecting previously unselected package r-bioc-delayedarray.
688s Preparing to unpack .../376-r-bioc-delayedarray_0.30.1+dfsg-1_amd64.deb ...
688s Unpacking r-bioc-delayedarray (0.30.1+dfsg-1) ...
688s Selecting previously unselected package r-bioc-genomicranges.
688s Preparing to unpack .../377-r-bioc-genomicranges_1.56.1+dfsg-1_amd64.deb ...
688s Unpacking r-bioc-genomicranges (1.56.1+dfsg-1) ...
688s Selecting previously unselected package r-bioc-summarizedexperiment.
688s Preparing to unpack .../378-r-bioc-summarizedexperiment_1.34.0+dfsg-1_all.deb ...
688s Unpacking r-bioc-summarizedexperiment (1.34.0+dfsg-1) ...
688s Selecting previously unselected package r-cran-locfit.
688s Preparing to unpack .../379-r-cran-locfit_1.5-9.9-1_amd64.deb ...
688s Unpacking r-cran-locfit (1.5-9.9-1) ...
688s Selecting previously unselected package r-cran-gtable.
688s Preparing to unpack .../380-r-cran-gtable_0.3.5+dfsg-1_all.deb ...
688s Unpacking r-cran-gtable (0.3.5+dfsg-1) ...
688s Selecting previously unselected package r-cran-isoband.
688s Preparing to unpack .../381-r-cran-isoband_0.2.7-1_amd64.deb ...
688s Unpacking r-cran-isoband (0.2.7-1) ...
688s Selecting previously unselected package r-cran-mass.
688s Preparing to unpack .../382-r-cran-mass_7.3-61-1_amd64.deb ...
688s Unpacking r-cran-mass (7.3-61-1) ...
688s Selecting previously unselected package r-cran-nlme.
689s Preparing to unpack .../383-r-cran-nlme_3.1.166-1_amd64.deb ...
689s Unpacking r-cran-nlme (3.1.166-1) ...
689s Selecting previously unselected package r-cran-mgcv.
689s Preparing to unpack .../384-r-cran-mgcv_1.9-1-1_amd64.deb ...
689s Unpacking r-cran-mgcv (1.9-1-1) ...
689s Selecting previously unselected package r-cran-farver.
689s Preparing to unpack .../385-r-cran-farver_2.1.2-1_amd64.deb ...
689s Unpacking r-cran-farver (2.1.2-1) ...
689s Selecting previously unselected package r-cran-labeling.
689s Preparing to unpack .../386-r-cran-labeling_0.4.3-1_all.deb ...
689s Unpacking r-cran-labeling (0.4.3-1) ...
689s Selecting previously unselected package r-cran-colorspace.
689s Preparing to unpack .../387-r-cran-colorspace_2.1-0+dfsg-1_amd64.deb ...
689s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ...
689s Selecting previously unselected package r-cran-munsell.
689s Preparing to unpack .../388-r-cran-munsell_0.5.1-1_all.deb ...
689s Unpacking r-cran-munsell (0.5.1-1) ...
689s Selecting previously unselected package r-cran-rcolorbrewer.
689s Preparing to unpack .../389-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ...
689s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ...
689s Selecting previously unselected package r-cran-viridislite.
689s Preparing to unpack .../390-r-cran-viridislite_0.4.2-2_all.deb ...
689s Unpacking r-cran-viridislite (0.4.2-2) ...
689s Selecting previously unselected package r-cran-scales.
689s Preparing to unpack .../391-r-cran-scales_1.3.0-1_all.deb ...
689s Unpacking r-cran-scales (1.3.0-1) ...
689s Selecting previously unselected package r-cran-ggplot2.
689s Preparing to unpack .../392-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ...
689s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ...
689s Selecting previously unselected package r-cran-rcpparmadillo.
689s Preparing to unpack .../393-r-cran-rcpparmadillo_14.0.0-1-1_amd64.deb ...
689s Unpacking r-cran-rcpparmadillo (14.0.0-1-1) ...
689s Selecting previously unselected package r-bioc-deseq2.
689s Preparing to unpack .../394-r-bioc-deseq2_1.44.0+dfsg-1_amd64.deb ...
689s Unpacking r-bioc-deseq2 (1.44.0+dfsg-1) ...
689s Selecting previously unselected package r-cran-hwriter.
689s Preparing to unpack .../395-r-cran-hwriter_1.3.2.1-1_all.deb ...
689s Unpacking r-cran-hwriter (1.3.2.1-1) ...
689s Selecting previously unselected package r-cran-bitops.
689s Preparing to unpack .../396-r-cran-bitops_1.0-7-1_amd64.deb ...
689s Unpacking r-cran-bitops (1.0-7-1) ...
689s Selecting previously unselected package r-bioc-rhtslib.
689s Preparing to unpack .../397-r-bioc-rhtslib_3.0.0+dfsg-1_amd64.deb ...
689s Unpacking r-bioc-rhtslib (3.0.0+dfsg-1) ...
689s Selecting previously unselected package r-bioc-rsamtools.
690s Preparing to unpack .../398-r-bioc-rsamtools_2.20.0+dfsg-1_amd64.deb ...
690s Unpacking r-bioc-rsamtools (2.20.0+dfsg-1) ...
690s Selecting previously unselected package r-cran-statmod.
690s Preparing to unpack .../399-r-cran-statmod_1.5.0-1_amd64.deb ...
690s Unpacking r-cran-statmod (1.5.0-1) ...
690s Selecting previously unselected package r-bioc-geneplotter.
690s Preparing to unpack .../400-r-bioc-geneplotter_1.82.0+dfsg-1_all.deb ...
690s Unpacking r-bioc-geneplotter (1.82.0+dfsg-1) ...
690s Selecting previously unselected package r-cran-survival.
690s Preparing to unpack .../401-r-cran-survival_3.7-0-1_amd64.deb ...
690s Unpacking r-cran-survival (3.7-0-1) ...
690s Selecting previously unselected package r-bioc-genefilter.
690s Preparing to unpack .../402-r-bioc-genefilter_1.86.0-1_amd64.deb ...
690s Unpacking r-bioc-genefilter (1.86.0-1) ...
690s Selecting previously unselected package r-bioc-dexseq.
690s Preparing to unpack .../403-r-bioc-dexseq_1.50.0+dfsg-1_all.deb ...
690s Unpacking r-bioc-dexseq (1.50.0+dfsg-1) ...
690s Selecting previously unselected package r-bioc-limma.
690s Preparing to unpack .../404-r-bioc-limma_3.60.4+dfsg-1_amd64.deb ...
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690s Selecting previously unselected package r-bioc-edger.
690s Preparing to unpack .../405-r-bioc-edger_4.2.1+dfsg-1_amd64.deb ...
690s Unpacking r-bioc-edger (4.2.1+dfsg-1) ...
690s Selecting previously unselected package r-bioc-genomicalignments.
690s Preparing to unpack .../406-r-bioc-genomicalignments_1.40.0-1_amd64.deb ...
690s Unpacking r-bioc-genomicalignments (1.40.0-1) ...
690s Selecting previously unselected package r-cran-rcurl.
690s Preparing to unpack .../407-r-cran-rcurl_1.98-1.14+dfsg-1build2_amd64.deb ...
690s Unpacking r-cran-rcurl (1.98-1.14+dfsg-1build2) ...
690s Selecting previously unselected package r-cran-rjson.
690s Preparing to unpack .../408-r-cran-rjson_0.2.21-1_amd64.deb ...
690s Unpacking r-cran-rjson (0.2.21-1) ...
690s Selecting previously unselected package r-cran-restfulr.
690s Preparing to unpack .../409-r-cran-restfulr_0.0.15-1_amd64.deb ...
690s Unpacking r-cran-restfulr (0.0.15-1) ...
690s Selecting previously unselected package r-bioc-rtracklayer.
690s Preparing to unpack .../410-r-bioc-rtracklayer_1.64.0-1_amd64.deb ...
690s Unpacking r-bioc-rtracklayer (1.64.0-1) ...
690s Selecting previously unselected package r-bioc-genomicfeatures.
690s Preparing to unpack .../411-r-bioc-genomicfeatures_1.56.0+dfsg-1_all.deb ...
690s Unpacking r-bioc-genomicfeatures (1.56.0+dfsg-1) ...
690s Selecting previously unselected package r-bioc-txdbmaker.
690s Preparing to unpack .../412-r-bioc-txdbmaker_1.0.1+ds-1_all.deb ...
690s Unpacking r-bioc-txdbmaker (1.0.1+ds-1) ...
690s Selecting previously unselected package r-bioc-genelendatabase.
690s Preparing to unpack .../413-r-bioc-genelendatabase_1.40.1-1_all.deb ...
690s Unpacking r-bioc-genelendatabase (1.40.1-1) ...
691s Selecting previously unselected package r-bioc-go.db.
691s Preparing to unpack .../414-r-bioc-go.db_3.19.1-1_all.deb ...
691s Unpacking r-bioc-go.db (3.19.1-1) ...
691s Selecting previously unselected package r-cran-biasedurn.
691s Preparing to unpack .../415-r-cran-biasedurn_2.0.11-1_amd64.deb ...
691s Unpacking r-cran-biasedurn (2.0.11-1) ...
691s Selecting previously unselected package r-bioc-goseq.
691s Preparing to unpack .../416-r-bioc-goseq_1.56.0-1_all.deb ...
691s Unpacking r-bioc-goseq (1.56.0-1) ...
691s Selecting previously unselected package r-cran-plyr.
691s Preparing to unpack .../417-r-cran-plyr_1.8.9-1_amd64.deb ...
691s Unpacking r-cran-plyr (1.8.9-1) ...
691s Selecting previously unselected package r-cran-reshape2.
691s Preparing to unpack .../418-r-cran-reshape2_1.4.4-2build1_amd64.deb ...
691s Unpacking r-cran-reshape2 (1.4.4-2build1) ...
691s Selecting previously unselected package r-bioc-qvalue.
691s Preparing to unpack .../419-r-bioc-qvalue_2.36.0-1_all.deb ...
691s Unpacking r-bioc-qvalue (2.36.0-1) ...
692s Selecting previously unselected package r-cran-findpython.
692s Preparing to unpack .../420-r-cran-findpython_1.0.8-1_all.deb ...
692s Unpacking r-cran-findpython (1.0.8-1) ...
692s Selecting previously unselected package r-cran-argparse.
692s Preparing to unpack .../421-r-cran-argparse_2.2.3+dfsg-1_all.deb ...
692s Unpacking r-cran-argparse (2.2.3+dfsg-1) ...
692s Selecting previously unselected package r-cran-backports.
692s Preparing to unpack .../422-r-cran-backports_1.5.0-2_amd64.deb ...
692s Unpacking r-cran-backports (1.5.0-2) ...
692s Selecting previously unselected package r-cran-broom.
692s Preparing to unpack .../423-r-cran-broom_1.0.6+dfsg-1_all.deb ...
692s Unpacking r-cran-broom (1.0.6+dfsg-1) ...
692s Selecting previously unselected package r-cran-ps.
692s Preparing to unpack .../424-r-cran-ps_1.7.6-1_amd64.deb ...
692s Unpacking r-cran-ps (1.7.6-1) ...
692s Selecting previously unselected package r-cran-processx.
692s Preparing to unpack .../425-r-cran-processx_3.8.4-1_amd64.deb ...
692s Unpacking r-cran-processx (3.8.4-1) ...
692s Selecting previously unselected package r-cran-callr.
692s Preparing to unpack .../426-r-cran-callr_3.7.6-1_all.deb ...
692s Unpacking r-cran-callr (3.7.6-1) ...
692s Selecting previously unselected package r-cran-rematch.
692s Preparing to unpack .../427-r-cran-rematch_2.0.0-1_all.deb ...
692s Unpacking r-cran-rematch (2.0.0-1) ...
692s Selecting previously unselected package r-cran-cellranger.
692s Preparing to unpack .../428-r-cran-cellranger_1.1.0-3_all.deb ...
692s Unpacking r-cran-cellranger (1.1.0-3) ...
692s Selecting previously unselected package r-cran-clipr.
692s Preparing to unpack .../429-r-cran-clipr_0.8.0-1_all.deb ...
692s Unpacking r-cran-clipr (0.8.0-1) ...
692s Selecting previously unselected package r-cran-cluster.
692s Preparing to unpack .../430-r-cran-cluster_2.1.6-1build1_amd64.deb ...
692s Unpacking r-cran-cluster (2.1.6-1build1) ...
692s Selecting previously unselected package r-cran-conflicted.
692s Preparing to unpack .../431-r-cran-conflicted_1.2.0-1.1_all.deb ...
692s Unpacking r-cran-conflicted (1.2.0-1.1) ...
692s Selecting previously unselected package r-cran-data.table.
692s Preparing to unpack .../432-r-cran-data.table_1.15.4+dfsg-2.2_amd64.deb ...
692s Unpacking r-cran-data.table (1.15.4+dfsg-2.2) ...
692s Selecting previously unselected package r-cran-dtplyr.
692s Preparing to unpack .../433-r-cran-dtplyr_1.3.1-1_all.deb ...
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692s Selecting previously unselected package r-cran-ellipsis.
692s Preparing to unpack .../434-r-cran-ellipsis_0.3.2-2_amd64.deb ...
692s Unpacking r-cran-ellipsis (0.3.2-2) ...
692s Selecting previously unselected package r-cran-fastcluster.
692s Preparing to unpack .../435-r-cran-fastcluster_1.2.6-1build1_amd64.deb ...
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692s Selecting previously unselected package r-cran-forcats.
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692s Selecting previously unselected package r-cran-gargle.
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692s Selecting previously unselected package r-cran-ggdendro.
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692s Unpacking r-cran-ggdendro (0.2.0+dfsg-1) ...
692s Selecting previously unselected package r-cran-uuid.
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693s Selecting previously unselected package r-cran-googledrive.
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693s Unpacking r-cran-googledrive (2.1.1-1) ...
693s Selecting previously unselected package r-cran-ids.
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693s Unpacking r-cran-ids (1.0.1-2) ...
693s Selecting previously unselected package r-cran-rematch2.
693s Preparing to unpack .../442-r-cran-rematch2_2.1.2-2build1_all.deb ...
693s Unpacking r-cran-rematch2 (2.1.2-2build1) ...
693s Selecting previously unselected package r-cran-googlesheets4.
693s Preparing to unpack .../443-r-cran-googlesheets4_1.1.1-1_all.deb ...
693s Unpacking r-cran-googlesheets4 (1.1.1-1) ...
693s Selecting previously unselected package r-cran-gridextra.
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693s Unpacking r-cran-gridextra (2.3-3build1) ...
693s Selecting previously unselected package r-cran-goplot.
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693s Selecting previously unselected package r-cran-tzdb.
693s Preparing to unpack .../446-r-cran-tzdb_0.4.0-2_amd64.deb ...
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693s Selecting previously unselected package r-cran-vroom.
693s Preparing to unpack .../447-r-cran-vroom_1.6.5-1_amd64.deb ...
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693s Selecting previously unselected package r-cran-readr.
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693s Selecting previously unselected package r-cran-haven.
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693s Selecting previously unselected package r-cran-kernsmooth.
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693s Selecting previously unselected package r-cran-timechange.
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693s Selecting previously unselected package r-cran-lubridate.
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693s Selecting previously unselected package r-cran-modelr.
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693s Selecting previously unselected package r-cran-systemfonts.
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693s Selecting previously unselected package r-cran-textshaping.
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693s Unpacking r-cran-textshaping (0.3.7-2) ...
693s Selecting previously unselected package r-cran-ragg.
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694s Selecting previously unselected package r-cran-readxl.
694s Preparing to unpack .../457-r-cran-readxl_1.4.3-1_amd64.deb ...
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694s Selecting previously unselected package r-cran-rstudioapi.
694s Preparing to unpack .../458-r-cran-rstudioapi_0.16.0-1_all.deb ...
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694s Selecting previously unselected package r-cran-reprex.
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694s Selecting previously unselected package r-cran-selectr.
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694s Selecting previously unselected package r-cran-rvest.
694s Preparing to unpack .../461-r-cran-rvest_1.0.4-1_all.deb ...
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694s Selecting previously unselected package r-cran-tidyverse.
694s Preparing to unpack .../462-r-cran-tidyverse_2.0.0+dfsg-1_all.deb ...
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694s Selecting previously unselected package bowtie.
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694s Unpacking bowtie (1.3.1-3) ...
694s Selecting previously unselected package bowtie2.
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694s Selecting previously unselected package trinityrnaseq.
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697s Setting up libhtscodecs2:amd64 (1.6.0-1build1) ...
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697s Setting up libxcb-dri3-0:amd64 (1.17.0-2) ...
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697s Setting up ncbi-data (6.1.20170106+dfsg2-3) ...
697s Setting up libtbbmalloc2:amd64 (2021.12.0-1ubuntu2) ...
697s Setting up libboost-program-options1.83.0:amd64 (1.83.0-3.2ubuntu2) ...
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697s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ...
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697s Setting up libmbedcrypto7t64:amd64 (2.28.8-1) ...
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698s update-language: texlive-base not installed and configured, doing nothing!
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698s Setting up librhino-java (1.7.14-2.1) ...
698s Setting up libblas3:amd64 (3.12.0-3build2) ...
698s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
698s Setting up libasound2t64:amd64 (1.2.12-1) ...
698s Setting up libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.2build1) ...
698s Setting up libepoxy0:amd64 (1.5.10-1build1) ...
698s Setting up libxfixes3:amd64 (1:6.0.0-2build1) ...
698s Setting up libxcb-sync1:amd64 (1.17.0-2) ...
698s Setting up libboost-iostreams1.83.0:amd64 (1.83.0-3.2ubuntu2) ...
698s Setting up libteckit0:amd64 (2.5.12+ds1-1) ...
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698s Setting up libavahi-common-data:amd64 (0.8-13ubuntu6) ...
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698s Setting up libhwloc15:amd64 (2.11.0-2) ...
698s Setting up libio-html-perl (1.004-3) ...
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698s Setting up libjbzip2-java (0.9.1-8) ...
698s Setting up libpcsclite1:amd64 (2.3.0-1) ...
698s Setting up libmongodb-java (3.6.3-2) ...
698s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ...
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698s Setting up berkeley-express (1.5.3+dfsg-3build5) ...
698s Setting up libvulkan1:amd64 (1.3.290.0-1) ...
698s Setting up libwebp7:amd64 (1.4.0-0.1) ...
698s Setting up libtimedate-perl (2.3300-2) ...
698s Setting up libubsan1:amd64 (14.2.0-7ubuntu1) ...
698s Setting up libxcb-dri2-0:amd64 (1.17.0-2) ...
698s Setting up libgif7:amd64 (5.2.2-1ubuntu1) ...
698s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
698s Setting up libjs-highlight.js (9.18.5+dfsg1-2) ...
698s Setting up hisat2 (2.2.1-5) ...
698s Setting up libfreemarker-java (2.3.32-2) ...
698s Setting up libxshmfence1:amd64 (1.3-1build5) ...
698s Setting up libhwasan0:amd64 (14.2.0-7ubuntu1) ...
698s Setting up subread (2.0.6+dfsg-3) ...
698s Setting up at-spi2-common (2.54.0-1) ...
698s Setting up libxcb-randr0:amd64 (1.17.0-2) ...
698s Setting up libasan8:amd64 (14.2.0-7ubuntu1) ...
698s Setting up libhts3t64:amd64 (1.20+ds-2) ...
698s Setting up fonts-lmodern (2.005-1) ...
698s Setting up liblua5.4-0:amd64 (5.4.6-3build2) ...
698s Setting up libharfbuzz0b:amd64 (9.0.0-1) ...
698s Setting up ncbi-vdb-data (3.0.2+dfsg-2build2) ...
698s Setting up libthai-data (0.1.29-2build1) ...
698s Setting up node-bootstrap-sass (3.4.3-2) ...
698s Setting up libcommons-math3-java (3.6.1-3) ...
698s Setting up libjs-prettify (2015.12.04+dfsg-1.1) ...
698s Setting up libwayland-egl1:amd64 (1.23.0-1) ...
698s Setting up libxss1:amd64 (1:1.2.3-1build3) ...
698s Setting up libjs-bootstrap4 (4.6.1+dfsg1-4) ...
698s Setting up libhttpcore-java (4.4.16-1) ...
698s Setting up pandoc-data (3.1.11.1-3) ...
698s Setting up libtsan2:amd64 (14.2.0-7ubuntu1) ...
698s Setting up libjoptsimple-java (5.0.4-4) ...
698s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
698s Setting up ca-certificates-java (20240118) ...
698s No JRE found. Skipping Java certificates setup.
698s Setting up node-normalize.css (8.0.1-5) ...
698s Setting up kallisto (0.48.0+dfsg-4build1) ...
698s Setting up libsnappy-jni (1.1.10.5-2) ...
698s Setting up libxcomposite1:amd64 (1:0.4.5-1build3) ...
698s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
698s Setting up xdg-utils (1.2.1-0ubuntu1) ...
698s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
698s Setting up liburi-perl (5.28-1) ...
698s Setting up liblsan0:amd64 (14.2.0-7ubuntu1) ...
698s Setting up libjs-bootstrap (3.4.1+dfsg-3) ...
698s Setting up libitm1:amd64 (14.2.0-7ubuntu1) ...
698s Setting up libsynctex2:amd64 (2024.20240313.70630+ds-4) ...
698s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
698s Setting up libdrm-amdgpu1:amd64 (2.4.122-1) ...
698s Setting up libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ...
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698s Setting up libwayland-client0:amd64 (1.23.0-1) ...
698s Setting up libnet-ssleay-perl:amd64 (1.94-2) ...
698s Setting up libjpeg8:amd64 (8c-2ubuntu11) ...
698s Setting up libice6:amd64 (2:1.0.10-1build3) ...
698s Setting up libhttp-date-perl (6.06-1) ...
698s Setting up parafly (0.1.0-4) ...
698s Setting up mesa-libgallium:amd64 (24.2.3-1ubuntu1) ...
698s Setting up liblapack3:amd64 (3.12.0-3build2) ...
698s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
698s Setting up libmbedx509-1t64:amd64 (2.28.8-1) ...
698s Setting up python3-pysam (0.22.1+ds-2) ...
698s Setting up libatk1.0-0t64:amd64 (2.54.0-1) ...
698s Setting up libfile-listing-perl (6.16-1) ...
698s Setting up python3-hisat2 (2.2.1-5) ...
698s Setting up openjdk-21-jre-headless:amd64 (21.0.5+11-1) ...
698s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode
698s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
698s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
698s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
698s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
698s Setting up libgbm1:amd64 (24.2.3-1ubuntu1) ...
698s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
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698s Setting up libxcursor1:amd64 (1:1.2.2-1) ...
698s Setting up libgl1-mesa-dri:amd64 (24.2.3-1ubuntu1) ...
698s Setting up libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ...
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698s Setting up libavahi-common3:amd64 (0.8-13ubuntu6) ...
698s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ...
698s Setting up libnet-http-perl (6.23-1) ...
698s Setting up dconf-service (0.40.0-4build2) ...
698s Setting up libbibtex-parser-perl (1.04+dfsg-1) ...
698s Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ...
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698s Setting up libcommons-jexl2-java (2.1.1-6) ...
698s Setting up libthai0:amd64 (0.1.29-2build1) ...
698s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
698s Setting up libptexenc1:amd64 (2024.20240313.70630+ds-4) ...
698s Setting up pandoc (3.1.11.1+ds-2) ...
698s Setting up jellyfish (2.3.1-3build2) ...
698s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
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700s Setting up libhtml-parser-perl:amd64 (3.83-1build1) ...
700s Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1) ...
700s Setting up libsnappy-java (1.1.10.5-2) ...
700s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ...
700s Setting up libgcc-14-dev:amd64 (14.2.0-7ubuntu1) ...
700s Setting up libcommons-codec-java (1.16.0-1) ...
700s Setting up libstdc++-14-dev:amd64 (14.2.0-7ubuntu1) ...
700s Setting up libsm6:amd64 (2:1.2.3-1build3) ...
700s Setting up python3-htseq (2.0.5-2) ...
700s /usr/lib/python3/dist-packages/HTSeq/__init__.py:583: SyntaxWarning: invalid escape sequence '\='
700s   _re_vcf_meta_comment = re.compile("^##([a-zA-Z]+)\=(.*)$")
700s /usr/lib/python3/dist-packages/HTSeq/features.py:14: SyntaxWarning: invalid escape sequence '\s'
700s   _re_attr_main = re.compile("\s*([^\s\=]+)[\s=]+(.*)")
700s /usr/lib/python3/dist-packages/HTSeq/features.py:15: SyntaxWarning: invalid escape sequence '\s'
700s   _re_attr_empty = re.compile("^\s*$")
700s /usr/lib/python3/dist-packages/HTSeq/features.py:16: SyntaxWarning: invalid escape sequence '\s'
700s   _re_gff_meta_comment = re.compile("##\s*(\S+)\s+(\S*)")
700s Setting up libavahi-client3:amd64 (0.8-13ubuntu6) ...
700s Setting up libio-socket-ssl-perl (2.088-1) ...
700s Setting up libhttp-message-perl (6.46-1ubuntu1) ...
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702s Setting up libcairo2:amd64 (1.18.2-2) ...
702s Setting up ncbi-blast+ (2.16.0+ds-6) ...
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702s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ...
702s Setting up libhttpclient-java (4.5.14-1) ...
702s Setting up liblightcouch-java (0.2.0-1) ...
702s Setting up libcairo-gobject2:amd64 (1.18.2-2) ...
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702s Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-2) ...
702s Setting up libcups2t64:amd64 (2.4.10-1ubuntu2) ...
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702s Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-2) ...
702s Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-9ubuntu1) ...
702s Setting up libngs-jni:amd64 (3.0.3+dfsg-9ubuntu1) ...
702s Setting up libxmu6:amd64 (2:1.1.3-3build2) ...
702s Setting up liblog4j2-java (2.19.0-2) ...
702s Setting up libxaw7:amd64 (2:1.0.14-1build2) ...
702s Setting up r-base-core (4.4.1-1) ...
702s 
702s Creating config file /etc/R/Renviron with new version
702s Setting up r-cran-crayon (1.5.2-1) ...
702s Setting up r-cran-labeling (0.4.3-1) ...
702s Setting up r-cran-biasedurn (2.0.11-1) ...
702s Setting up r-cran-sourcetools (0.1.7-1-1) ...
702s Setting up r-cran-futile.options (1.0.1-3build1) ...
702s Setting up r-cran-lattice (0.22-6-1) ...
702s Setting up r-cran-ps (1.7.6-1) ...
702s Setting up r-cran-nlme (3.1.166-1) ...
702s Setting up r-cran-farver (2.1.2-1) ...
702s Setting up r-cran-formatr (1.14-2) ...
702s Setting up r-cran-xml (3.99-0.17-1) ...
702s Setting up trinityrnaseq-examples (2.15.1+dfsg-5build1) ...
702s Setting up r-cran-viridislite (0.4.2-2) ...
703s Setting up r-cran-locfit (1.5-9.9-1) ...
703s Setting up texlive-binaries (2024.20240313.70630+ds-4) ...
703s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
703s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
703s Setting up r-cran-cluster (2.1.6-1build1) ...
703s Setting up rsem (1.3.3+dfsg-3build1) ...
703s Setting up r-cran-statmod (1.5.0-1) ...
703s Setting up r-cran-clipr (0.8.0-1) ...
703s Setting up r-cran-commonmark (1.9.1-1) ...
703s Setting up libngs-java:amd64 (3.0.3+dfsg-9ubuntu1) ...
703s Setting up r-cran-r6 (2.5.1-1) ...
703s Setting up r-cran-pkgkitten (0.2.4-1) ...
703s Setting up r-cran-fastcluster (1.2.6-1build1) ...
703s Setting up texlive-base (2024.20240706-1) ...
703s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps
703s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg
704s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper
704s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex
704s Setting up r-cran-magrittr (2.0.3-1) ...
704s Setting up r-cran-rappdirs (0.3.3-1) ...
704s Setting up r-cran-filelock (1.0.3-1) ...
704s Setting up libhtsjdk-java (4.1.0+dfsg-2) ...
704s Setting up libbarclay-java (5.0.0+dfsg-1) ...
704s Setting up r-bioc-genomeinfodbdata (1.2.12-1) ...
704s Setting up r-cran-littler (0.3.20-1) ...
704s Setting up r-cran-bh (1.84.0-1) ...
704s Setting up r-cran-fs (1.6.4+dfsg-1) ...
704s Setting up r-cran-rcpp (1.0.13-1) ...
704s Setting up r-cran-curl (5.2.1+dfsg-1) ...
704s Setting up r-cran-codetools (0.2-20-1) ...
704s Setting up r-cran-rematch (2.0.0-1) ...
704s Setting up r-bioc-biocgenerics (0.50.0-2) ...
704s Setting up r-cran-rlang (1.1.4-1) ...
704s Setting up r-cran-matrixstats (1.3.0-1) ...
704s Setting up r-cran-findpython (1.0.8-1) ...
704s Setting up littler (0.3.20-1) ...
704s Setting up r-bioc-matrixgenerics (1.16.0-2) ...
704s Setting up r-cran-uuid (1.2-1-1) ...
704s Setting up r-cran-xfun (0.45+dfsg-1) ...
704s Setting up r-cran-sys (3.4.2-1) ...
704s Setting up r-cran-plogr (0.2.0-3build1) ...
704s Setting up r-cran-withr (3.0.0+dfsg-1) ...
704s Setting up r-cran-backports (1.5.0-2) ...
704s Setting up libgkl-java (0.8.11+dfsg-2build1) ...
704s Setting up r-cran-processx (3.8.4-1) ...
704s Setting up r-cran-mime (0.12-2) ...
704s Setting up r-cran-generics (0.1.3-1) ...
704s Setting up r-cran-base64enc (0.1-3-3) ...
704s Setting up r-cran-abind (1.4-5-2) ...
704s Setting up r-cran-digest (0.6.36-1) ...
704s Setting up r-cran-yaml (2.3.8-2) ...
704s Setting up r-cran-lambda.r (1.2.4-2build1) ...
704s Setting up r-cran-evaluate (0.24.0-1) ...
704s Setting up r-cran-dbi (1.2.3-1) ...
704s Setting up r-cran-highr (0.11+dfsg-1) ...
704s Setting up r-cran-prettyunits (1.2.0-1) ...
704s Setting up r-cran-fansi (1.0.5-1) ...
704s Setting up r-cran-mass (7.3-61-1) ...
704s Setting up r-cran-snow (1:0.4.4-2) ...
704s Setting up r-cran-data.table (1.15.4+dfsg-2.2) ...
704s Setting up r-cran-glue (1.7.0-1) ...
704s Setting up r-cran-bit (4.0.5-1) ...
704s Setting up r-cran-xtable (1:1.8-4-2) ...
704s Setting up r-cran-cli (3.6.2-1) ...
704s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
704s Setting up r-cran-bitops (1.0-7-1) ...
704s Setting up r-bioc-biocversion (3.19.1-1) ...
704s Setting up r-cran-bit64 (4.0.5-1) ...
704s Setting up r-cran-biocmanager (1.30.22+dfsg-2) ...
704s Setting up r-bioc-zlibbioc (1.50.0+dfsg-2) ...
704s Setting up r-cran-askpass (1.2.0-1) ...
704s Setting up r-cran-fastmap (1.1.1-1) ...
704s Setting up r-cran-png (0.1-8-1build2) ...
704s Setting up r-bioc-biobase (2.64.0-4) ...
704s Setting up r-cran-jsonlite (1.8.8+dfsg-1) ...
704s Setting up r-cran-rstudioapi (0.16.0-1) ...
704s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
704s Setting up libpicard-java (3.1.1+dfsg-1) ...
704s Setting up r-cran-utf8 (1.2.4-1) ...
704s Setting up r-cran-colorspace (2.1-0+dfsg-1) ...
704s Setting up r-cran-stringi (1.8.3-1) ...
704s Setting up texlive-latex-base (2024.20240706-1) ...
704s Setting up r-cran-hwriter (1.3.2.1-1) ...
704s Setting up r-cran-cpp11 (0.4.7-1) ...
704s Setting up r-cran-plyr (1.8.9-1) ...
704s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ...
704s Setting up r-bioc-s4vectors (0.42.1+dfsg-2) ...
704s Setting up r-cran-isoband (0.2.7-1) ...
704s Setting up r-cran-futile.logger (1.4.3-4build1) ...
704s Setting up r-bioc-limma (3.60.4+dfsg-1) ...
704s Setting up r-cran-gtable (0.3.5+dfsg-1) ...
704s Setting up r-cran-later (1.3.2+dfsg-1) ...
704s Setting up r-cran-matrix (1.7-0-3) ...
704s Setting up r-cran-htmltools (0.5.8.1-1) ...
704s Setting up r-cran-tinytex (0.51-1) ...
704s Setting up r-cran-kernsmooth (2.23-24-1) ...
704s Setting up r-cran-knitr (1.47+dfsg-1) ...
704s Setting up r-cran-mgcv (1.9-1-1) ...
704s Setting up r-cran-cachem (1.0.8-1) ...
704s Setting up r-cran-sass (0.4.9+dfsg-1) ...
704s Setting up r-cran-rcpparmadillo (14.0.0-1-1) ...
704s Setting up r-bioc-iranges (2.38.1-1) ...
704s Setting up r-cran-rjson (0.2.21-1) ...
704s Setting up r-cran-tzdb (0.4.0-2) ...
704s Setting up r-cran-argparse (2.2.3+dfsg-1) ...
704s Setting up r-cran-rcurl (1.98-1.14+dfsg-1build2) ...
704s Setting up r-cran-restfulr (0.0.15-1) ...
704s Setting up r-cran-vctrs (0.6.5-1) ...
704s Setting up r-cran-pillar (1.9.0+dfsg-1) ...
704s Setting up r-cran-ellipsis (0.3.2-2) ...
704s Setting up r-cran-openssl (2.2.0+dfsg-1) ...
704s Setting up r-bioc-s4arrays (1.4.1+dfsg-1) ...
704s Setting up r-cran-stringr (1.5.1-1) ...
704s Setting up r-bioc-biocparallel (1.38.0-2) ...
704s Setting up r-cran-callr (3.7.6-1) ...
704s Setting up r-cran-selectr (0.4-2-2build1) ...
704s Setting up r-bioc-edger (4.2.1+dfsg-1) ...
704s Setting up r-bioc-rhtslib (3.0.0+dfsg-1) ...
704s Setting up r-cran-xml2 (1.3.6-1) ...
704s Setting up r-cran-munsell (0.5.1-1) ...
704s Setting up r-cran-tibble (3.2.1+dfsg-2) ...
704s Setting up r-cran-fontawesome (0.5.2-1) ...
704s Setting up r-cran-survival (3.7-0-1) ...
704s Setting up r-bioc-biocio (1.14.0+dfsg-1) ...
704s Setting up r-cran-forcats (1.0.0-1) ...
704s Setting up r-cran-jquerylib (0.1.4+dfsg-4) ...
704s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ...
704s Setting up texlive-bibtex-extra (2024.20240706-2) ...
704s Setting up r-cran-reshape2 (1.4.4-2build1) ...
704s Setting up r-cran-httr2 (1.0.2-1) ...
704s Setting up r-cran-systemfonts (1.1.0-1) ...
704s Setting up r-cran-ids (1.0.1-2) ...
704s Setting up r-cran-timechange (0.3.0-1) ...
704s Setting up r-cran-httr (1.4.7+dfsg-1) ...
704s Setting up r-cran-gridextra (2.3-3build1) ...
704s Setting up r-cran-hms (1.1.3-1) ...
704s Setting up r-cran-scales (1.3.0-1) ...
704s Setting up r-cran-memoise (2.0.1-1) ...
704s Setting up r-cran-promises (1.3.0+dfsg-1) ...
704s Setting up r-cran-purrr (1.0.2-1) ...
704s Setting up r-cran-blob (1.2.4-1) ...
704s Setting up r-bioc-xvector (0.44.0-1) ...
704s Setting up r-cran-dplyr (1.1.4-1) ...
704s Setting up r-cran-rsqlite (2.3.7-2) ...
704s Setting up r-cran-progress (1.2.3-1) ...
704s Setting up r-cran-lubridate (1.9.3+dfsg-1) ...
704s Setting up r-cran-gargle (1.5.2-1) ...
704s Setting up r-cran-vroom (1.6.5-1) ...
704s Setting up r-cran-conflicted (1.2.0-1.1) ...
704s Setting up r-bioc-ucsc.utils (1.0.0+ds-2) ...
704s Setting up r-bioc-sparsearray (1.4.8+dfsg-1) ...
704s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ...
704s Setting up r-cran-cellranger (1.1.0-3) ...
704s Setting up r-cran-httpuv (1.6.15+dfsg-1) ...
704s Setting up r-cran-rematch2 (2.1.2-2build1) ...
704s Setting up r-cran-textshaping (0.3.7-2) ...
704s Setting up r-cran-rvest (1.0.4-1) ...
704s Setting up r-cran-dtplyr (1.3.1-1) ...
704s Setting up r-bioc-genomeinfodb (1.40.1+dfsg-1) ...
704s Setting up r-cran-bslib (0.7.0+dfsg-1) ...
704s Setting up r-cran-ragg (1.3.2-1) ...
704s Setting up r-cran-readr (2.1.5-1) ...
704s Setting up r-cran-tidyr (1.3.1-1) ...
704s Setting up r-cran-ggdendro (0.2.0+dfsg-1) ...
704s Setting up r-cran-googledrive (2.1.1-1) ...
704s Setting up r-cran-googlesheets4 (1.1.1-1) ...
704s Setting up r-bioc-qvalue (2.36.0-1) ...
704s Setting up r-cran-dbplyr (2.4.0+dfsg-1) ...
704s Setting up r-bioc-delayedarray (0.30.1+dfsg-1) ...
704s Setting up r-cran-readxl (1.4.3-1) ...
704s Setting up r-bioc-biocfilecache (2.12.0+dfsg-1) ...
704s Setting up r-cran-haven (2.5.4-1) ...
704s Setting up r-bioc-genomicranges (1.56.1+dfsg-1) ...
704s Setting up r-bioc-biostrings (2.72.1+dfsg-1) ...
704s Setting up r-cran-shiny (1.8.1.1+dfsg-1) ...
704s Setting up r-cran-broom (1.0.6+dfsg-1) ...
704s Setting up r-cran-rmarkdown (2.27+dfsg-1) ...
704s Setting up r-cran-goplot (1.0.2-2) ...
704s Setting up r-bioc-rsamtools (2.20.0+dfsg-1) ...
704s Setting up r-cran-bookdown (0.40+dfsg-1) ...
704s Setting up r-cran-reprex (2.1.0-1) ...
704s Setting up r-bioc-summarizedexperiment (1.34.0+dfsg-1) ...
704s Setting up r-bioc-keggrest (1.44.1+dfsg-1) ...
704s Setting up r-bioc-deseq2 (1.44.0+dfsg-1) ...
704s Setting up r-bioc-annotationdbi (1.66.0-1) ...
704s Setting up r-bioc-go.db (3.19.1-1) ...
704s Setting up r-cran-modelr (0.1.11-1) ...
704s Setting up r-bioc-annotate (1.82.0+dfsg-1) ...
704s Setting up r-bioc-biomart (2.60.1+dfsg-1) ...
704s Setting up r-bioc-genefilter (1.86.0-1) ...
704s Setting up r-bioc-biocstyle (2.32.1+dfsg-1) ...
704s Setting up r-bioc-genomicalignments (1.40.0-1) ...
704s Setting up r-bioc-geneplotter (1.82.0+dfsg-1) ...
704s Setting up r-bioc-rtracklayer (1.64.0-1) ...
704s Setting up r-bioc-genomicfeatures (1.56.0+dfsg-1) ...
704s Setting up r-cran-tidyverse (2.0.0+dfsg-1) ...
704s Setting up r-bioc-dexseq (1.50.0+dfsg-1) ...
704s Setting up r-bioc-txdbmaker (1.0.1+ds-1) ...
704s Setting up r-bioc-genelendatabase (1.40.1-1) ...
704s Setting up r-bioc-goseq (1.56.0-1) ...
704s Setting up adwaita-icon-theme (47.0-1) ...
704s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
704s Setting up liblwp-protocol-https-perl (6.14-1) ...
704s Setting up liberror-prone-java (2.18.0-1) ...
704s Setting up libwww-perl (6.77-1) ...
704s Setting up humanity-icon-theme (0.6.16) ...
705s Setting up libguava-java (32.0.1-1) ...
705s Setting up ubuntu-mono (24.04-0ubuntu1) ...
705s Setting up libjung-free-java (2.1.1-2) ...
705s Processing triggers for libglib2.0-0t64:amd64 (2.82.1-0ubuntu1) ...
705s Setting up libgtk-3-0t64:amd64 (3.24.43-3ubuntu2) ...
705s Processing triggers for install-info (7.1.1-1) ...
705s Processing triggers for libc-bin (2.40-1ubuntu3) ...
705s Processing triggers for man-db (2.12.1-3) ...
706s Processing triggers for ca-certificates-java (20240118) ...
707s Adding debian:ACCVRAIZ1.pem
707s Adding debian:AC_RAIZ_FNMT-RCM.pem
707s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
707s Adding debian:ANF_Secure_Server_Root_CA.pem
707s Adding debian:Actalis_Authentication_Root_CA.pem
707s Adding debian:AffirmTrust_Commercial.pem
707s Adding debian:AffirmTrust_Networking.pem
707s Adding debian:AffirmTrust_Premium.pem
707s Adding debian:AffirmTrust_Premium_ECC.pem
707s Adding debian:Amazon_Root_CA_1.pem
707s Adding debian:Amazon_Root_CA_2.pem
707s Adding debian:Amazon_Root_CA_3.pem
707s Adding debian:Amazon_Root_CA_4.pem
707s Adding debian:Atos_TrustedRoot_2011.pem
707s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
707s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
707s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
707s Adding debian:BJCA_Global_Root_CA1.pem
707s Adding debian:BJCA_Global_Root_CA2.pem
707s Adding debian:Baltimore_CyberTrust_Root.pem
707s Adding debian:Buypass_Class_2_Root_CA.pem
707s Adding debian:Buypass_Class_3_Root_CA.pem
707s Adding debian:CA_Disig_Root_R2.pem
707s Adding debian:CFCA_EV_ROOT.pem
707s Adding debian:COMODO_Certification_Authority.pem
707s Adding debian:COMODO_ECC_Certification_Authority.pem
707s Adding debian:COMODO_RSA_Certification_Authority.pem
707s Adding debian:Certainly_Root_E1.pem
707s Adding debian:Certainly_Root_R1.pem
707s Adding debian:Certigna.pem
707s Adding debian:Certigna_Root_CA.pem
707s Adding debian:Certum_EC-384_CA.pem
707s Adding debian:Certum_Trusted_Network_CA.pem
707s Adding debian:Certum_Trusted_Network_CA_2.pem
707s Adding debian:Certum_Trusted_Root_CA.pem
707s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
707s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
707s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
707s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
707s Adding debian:Comodo_AAA_Services_root.pem
707s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
707s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
707s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
707s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
707s Adding debian:DigiCert_Assured_ID_Root_CA.pem
707s Adding debian:DigiCert_Assured_ID_Root_G2.pem
707s Adding debian:DigiCert_Assured_ID_Root_G3.pem
707s Adding debian:DigiCert_Global_Root_CA.pem
707s Adding debian:DigiCert_Global_Root_G2.pem
707s Adding debian:DigiCert_Global_Root_G3.pem
707s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
707s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
707s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
707s Adding debian:DigiCert_Trusted_Root_G4.pem
707s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
707s Adding debian:Entrust_Root_Certification_Authority.pem
707s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
707s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
707s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
707s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
707s Adding debian:GLOBALTRUST_2020.pem
707s Adding debian:GTS_Root_R1.pem
707s Adding debian:GTS_Root_R2.pem
707s Adding debian:GTS_Root_R3.pem
707s Adding debian:GTS_Root_R4.pem
707s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
707s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
707s Adding debian:GlobalSign_Root_CA.pem
707s Adding debian:GlobalSign_Root_CA_-_R3.pem
707s Adding debian:GlobalSign_Root_CA_-_R6.pem
707s Adding debian:GlobalSign_Root_E46.pem
707s Adding debian:GlobalSign_Root_R46.pem
707s Adding debian:Go_Daddy_Class_2_CA.pem
707s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
707s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
707s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
707s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
707s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
707s Adding debian:HiPKI_Root_CA_-_G1.pem
707s Adding debian:Hongkong_Post_Root_CA_3.pem
707s Adding debian:ISRG_Root_X1.pem
707s Adding debian:ISRG_Root_X2.pem
707s Adding debian:IdenTrust_Commercial_Root_CA_1.pem
707s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
707s Adding debian:Izenpe.com.pem
707s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
707s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
707s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
707s Adding debian:NAVER_Global_Root_Certification_Authority.pem
707s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
707s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
707s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
707s Adding debian:QuoVadis_Root_CA_1_G3.pem
707s Adding debian:QuoVadis_Root_CA_2.pem
707s Adding debian:QuoVadis_Root_CA_2_G3.pem
707s Adding debian:QuoVadis_Root_CA_3.pem
707s Adding debian:QuoVadis_Root_CA_3_G3.pem
707s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
707s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
707s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
707s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
707s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
707s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
707s Adding debian:SZAFIR_ROOT_CA2.pem
707s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
707s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
707s Adding debian:SecureSign_RootCA11.pem
707s Adding debian:SecureTrust_CA.pem
707s Adding debian:Secure_Global_CA.pem
707s Adding debian:Security_Communication_ECC_RootCA1.pem
707s Adding debian:Security_Communication_RootCA2.pem
707s Adding debian:Security_Communication_RootCA3.pem
707s Adding debian:Security_Communication_Root_CA.pem
707s Adding debian:Starfield_Class_2_CA.pem
707s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
707s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
707s Adding debian:SwissSign_Gold_CA_-_G2.pem
707s Adding debian:SwissSign_Silver_CA_-_G2.pem
707s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
707s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
707s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
707s Adding debian:TWCA_Global_Root_CA.pem
707s Adding debian:TWCA_Root_Certification_Authority.pem
707s Adding debian:TeliaSonera_Root_CA_v1.pem
707s Adding debian:Telia_Root_CA_v2.pem
707s Adding debian:TrustAsia_Global_Root_CA_G3.pem
707s Adding debian:TrustAsia_Global_Root_CA_G4.pem
707s Adding debian:Trustwave_Global_Certification_Authority.pem
707s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
707s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
707s Adding debian:TunTrust_Root_CA.pem
707s Adding debian:UCA_Extended_Validation_Root.pem
707s Adding debian:UCA_Global_G2_Root.pem
707s Adding debian:USERTrust_ECC_Certification_Authority.pem
707s Adding debian:USERTrust_RSA_Certification_Authority.pem
707s Adding debian:XRamp_Global_CA_Root.pem
707s Adding debian:certSIGN_ROOT_CA.pem
707s Adding debian:certSIGN_Root_CA_G2.pem
707s Adding debian:e-Szigno_Root_CA_2017.pem
707s Adding debian:ePKI_Root_Certification_Authority.pem
707s Adding debian:emSign_ECC_Root_CA_-_C3.pem
707s Adding debian:emSign_ECC_Root_CA_-_G3.pem
707s Adding debian:emSign_Root_CA_-_C1.pem
707s Adding debian:emSign_Root_CA_-_G1.pem
707s Adding debian:vTrus_ECC_Root_CA.pem
707s Adding debian:vTrus_Root_CA.pem
707s done.
707s Setting up default-jre-headless (2:1.21-76) ...
707s Setting up jaligner (1.0+dfsg-11) ...
707s Setting up openjdk-21-jre:amd64 (21.0.5+11-1) ...
707s Setting up default-jre (2:1.21-76) ...
707s Setting up trimmomatic (0.39+dfsg-2) ...
707s Setting up trinityrnaseq (2.15.1+dfsg-5build1) ...
707s Setting up autopkgtest-satdep (0) ...
707s Processing triggers for tex-common (6.18) ...
708s Running updmap-sys. This may take some time... done.
708s Running mktexlsr /var/lib/texmf ... done.
708s Building format(s) --all.
737s 	This may take some time... done.
751s (Reading database ... 147388 files and directories currently installed.)
751s Removing autopkgtest-satdep (0) ...
751s autopkgtest [14:10:17]: test run-tests: [-----------------------
751s cd test_Trinity_Assembly && make test_all
751s make[1]: Entering directory '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly'
751s ./runMe.sh
751s #!/bin/bash -ve
751s 
751s #######################################################
751s ##  Run Trinity to Generate Transcriptome Assemblies ##
751s #######################################################
751s 
751s if [ -z ${TRINITY_HOME} ]; then
751s     echo "Must set env var TRINITY_HOME"
751s     exit 1
751s fi
751s 
751s 
751s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \
751s               --left reads.left.fq.gz \
751s               --right reads.right.fq.gz \
751s               --SS_lib_type RF \
751s               --CPU 1 \
751s               --no_cleanup
751s 
751s 
751s      ______  ____   ____  ____   ____  ______  __ __
751s     |      ||    \ |    ||    \ |    ||      ||  |  |
751s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
751s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
751s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
751s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
751s       |__|  |__|\_||____||__|__||____|  |__|  |____/
751s 
751s     Trinity-v2.15.1
751s 
751s 
751s 
751s Left read files: $VAR1 = [
751s           'reads.left.fq.gz'
751s         ];
751s Right read files: $VAR1 = [
751s           'reads.right.fq.gz'
751s         ];
751s Monday, November 4, 2024: 14:10:17	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir
751s Monday, November 4, 2024: 14:10:17	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis
751s 
751s 
751s ----------------------------------------------------------------------------------
751s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
751s ----------------------------------------------------------------------------------
751s 
751s ---------------------------------------------------------------
751s ------------ In silico Read Normalization ---------------------
751s -- (Removing Excess Reads Beyond 200 Coverage --
751s ---------------------------------------------------------------
751s 
751s # running normalization on reads: $VAR1 = [
751s           [
751s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
751s           ],
751s           [
751s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
751s           ]
751s         ];
751s 
751s 
751s Monday, November 4, 2024: 14:10:17	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 1 --output /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together  --PARALLEL_STATS  
752s -prepping seqs
752s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
752s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
752s CMD finished (0 seconds)
752s CMD finished (0 seconds)
752s CMD: touch left.fa.ok
752s CMD finished (0 seconds)
752s CMD: touch right.fa.ok
752s CMD finished (0 seconds)
752s Done converting input files.CMD: cat left.fa right.fa > both.fa
752s CMD finished (0 seconds)
752s CMD: touch both.fa.ok
752s CMD finished (0 seconds)
752s -kmer counting.
752s -------------------------------------------
752s ----------- Jellyfish  --------------------
752s -- (building a k-mer catalog from reads) --
752s -------------------------------------------
752s 
752s CMD: jellyfish count -t 1 -m 25 -s 100000000  both.fa
754s CMD finished (2 seconds)
754s CMD: jellyfish histo -t 1 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
754s CMD finished (0 seconds)
754s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
754s CMD finished (0 seconds)
754s CMD: touch jellyfish.K25.min2.kmers.fa.success
754s CMD finished (0 seconds)
754s -generating stats files
754s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
754s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
754s -reading Kmer occurrences...
754s -reading Kmer occurrences...
754s 
754s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
754s 
754s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
755s STATS_GENERATION_TIME: 1 seconds.
755s CMD finished (1 seconds)
755s STATS_GENERATION_TIME: 1 seconds.
755s CMD finished (1 seconds)
755s CMD: touch left.fa.K25.stats.ok
755s CMD finished (0 seconds)
755s CMD: touch right.fa.K25.stats.ok
755s CMD finished (0 seconds)
755s -sorting each stats file by read name.
755s 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
755s 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
755s CMD finished (0 seconds)
755s CMD finished (0 seconds)
755s CMD: touch left.fa.K25.stats.sort.ok
755s CMD finished (0 seconds)
755s CMD: touch right.fa.K25.stats.sort.ok
755s CMD finished (0 seconds)
755s -defining normalized reads
755s 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
755s -opening left.fa.K25.stats.sort
755s -opening right.fa.K25.stats.sort
755s -done opening files.
755s CMD finished (0 seconds)
755s CMD: touch pairs.K25.stats.ok
755s CMD finished (0 seconds)
755s 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
755s 30472 / 30575 = 99.66% reads selected during normalization.
755s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
755s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
755s CMD finished (0 seconds)
755s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
755s CMD finished (0 seconds)
755s -search and capture.
755s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture.
755s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
755s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture.
755s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
756s CMD: touch /tmp/autopkgtest.vWCmNc/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
756s CMD finished (0 seconds)
756s CMD: touch /tmp/autopkgtest.vWCmNc/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
756s CMD finished (0 seconds)
756s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
756s CMD finished (0 seconds)
756s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
756s CMD finished (0 seconds)
756s 
756s 
756s Normalization complete. See outputs: 
756s 	/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
756s 	/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
756s Monday, November 4, 2024: 14:10:22	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/normalization.ok
756s Converting input files. (in parallel)Monday, November 4, 2024: 14:10:22	CMD: cat /tmp/autopkgtest.vWCmNc/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
756s Monday, November 4, 2024: 14:10:22	CMD: cat /tmp/autopkgtest.vWCmNc/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
756s Monday, November 4, 2024: 14:10:22	CMD: touch left.fa.ok
756s Monday, November 4, 2024: 14:10:22	CMD: touch right.fa.ok
756s Monday, November 4, 2024: 14:10:22	CMD: touch left.fa.ok right.fa.ok
756s Monday, November 4, 2024: 14:10:22	CMD: cat left.fa right.fa > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
756s Monday, November 4, 2024: 14:10:22	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa.ok
756s -------------------------------------------
756s ----------- Jellyfish  --------------------
756s -- (building a k-mer (25) catalog from reads) --
756s -------------------------------------------
756s 
756s * [Mon Nov  4 14:10:22 2024] Running CMD: jellyfish count -t 1 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
758s * [Mon Nov  4 14:10:24 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
758s * [Mon Nov  4 14:10:24 2024] Running CMD: jellyfish histo -t 1 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
759s ----------------------------------------------
759s --------------- Inchworm (K=25, asm) ---------------------
759s -- (Linear contig construction from k-mers) --
759s ----------------------------------------------
759s 
759s * [Mon Nov  4 14:10:25 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa.tmp
759s Kmer length set to: 25
759s Min assembly length set to: 25
759s Monitor turned on, set to: 1
759s -retaining tmp files
759s min entropy set to: 1
759s setting number of threads to: 1
759s -setting parallel iworm mode.
759s -reading Kmer occurrences...
759s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
759s  done parsing 519541 Kmers, 519541 added, taking 0 seconds.
759s 
759s TIMING KMER_DB_BUILDING 0 s.
759s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
759s Pruned 4252 kmers from catalog.
759s 	Pruning time: 0 seconds = 0 minutes.
759s 
759s TIMING PRUNING 0 s.
759s -populating the kmer seed candidate list.
759s Kcounter hash size: 519541
759s Processed 515289 non-zero abundance kmers in kcounter.
759s -Not sorting list of kmers, given parallel mode in effect.
759s -beginning inchworm contig assembly.
759s Total kcounter hash size: 519541 vs. sorted list size: 515289
759s num threads set to: 1
759s Done opening file. tmp.iworm.fa.pid_8513.thread_0
760s 
760s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
760s 
760s TIMING CONTIG_BUILDING 1 s.
760s 
760s TIMING PROG_RUNTIME 1 s.
760s * [Mon Nov  4 14:10:26 2024] Running CMD: mv /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa.tmp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa
760s Monday, November 4, 2024: 14:10:26	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa.finished
760s --------------------------------------------------------
760s -------------------- Chrysalis -------------------------
760s -- (Contig Clustering & de Bruijn Graph Construction) --
760s --------------------------------------------------------
760s 
760s inchworm_target: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
760s bowtie_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
760s chrysalis_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
760s * [Mon Nov  4 14:10:26 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa 100 10 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100
760s * [Mon Nov  4 14:10:26 2024] Running CMD: /usr/bin/bowtie2-build --threads 1 -o 3 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 1>/dev/null
760s * [Mon Nov  4 14:10:26 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" 
764s * [Mon Nov  4 14:10:30 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_scaffolds.txt
764s * [Mon Nov  4 14:10:30 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt
765s * [Mon Nov  4 14:10:31 2024] Running CMD: /usr/bin/sort --parallel=1 -T . -S 2G  -k9,9gr /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted
765s * [Mon Nov  4 14:10:31 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
765s * [Mon Nov  4 14:10:31 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/GraphFromIwormFasta.out
765s * [Mon Nov  4 14:10:31 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200
765s * [Mon Nov  4 14:10:31 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa -f /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/readsToComponents.out -t 1 -max_mem_reads 50000000  -strand  -p 10 
768s * [Mon Nov  4 14:10:34 2024] Running CMD: /usr/bin/sort --parallel=1 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/readsToComponents.out > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/readsToComponents.out.sort
768s Monday, November 4, 2024: 14:10:34	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/read_partitions/Fb_0/CBin_0
769s Monday, November 4, 2024: 14:10:35	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/partitioned_reads.files.list.ok
769s Monday, November 4, 2024: 14:10:35	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.vWCmNc/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
769s Monday, November 4, 2024: 14:10:35	CMD: touch recursive_trinity.cmds.ok
769s Monday, November 4, 2024: 14:10:35	CMD: touch recursive_trinity.cmds.ok
769s 
769s 
769s --------------------------------------------------------------------------------
769s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
769s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
769s --------------------------------------------------------------------------------
769s 
769s Monday, November 4, 2024: 14:10:35	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 1 -v -shuffle 
769s Number of Commands: 36
854s 
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.    
854s 
854s All commands completed successfully. :-)
854s 
854s 
854s 
854s ** Harvesting all assembled transcripts into a single multi-fasta file...
854s 
854s Monday, November 4, 2024: 14:12:00	CMD: find /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.tmp
854s * [Mon Nov  4 14:12:00 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa 1
856s * [Mon Nov  4 14:12:02 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta
856s Monday, November 4, 2024: 14:12:02	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta.gene_trans_map
856s 
856s 
856s #############################################################################
856s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta
856s #############################################################################
856s 
856s 
856s ./misc_run_tests/__test_runMe_NO_normalization.sh
856s 
856s ##### Done Running Trinity #####
856s 
856s if [ $* ]; then
856s     # check full-length reconstruction stats:
856s 
856s     ${TRINITY_HOME}/util/misc/illustrate_ref_comparison.pl __indiv_ex_sample_derived/refSeqs.fa trinity_out_dir.Trinity.fasta 90
856s 
856s     ./test_FL.sh --query  trinity_out_dir.Trinity.fasta --target __indiv_ex_sample_derived/refSeqs.fa --no_reuse
856s 
856s fi
856s 
856s #!/bin/bash -ve
856s 
856s 
856s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
856s     gunzip -c reads.right.fq.gz > reads.right.fq
856s fi
856s 
856s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
856s     gunzip -c reads.left.fq.gz > reads.left.fq
856s fi
856s 
856s 
856s 
856s #######################################################
856s ##  Run Trinity to Generate Transcriptome Assemblies ##
856s #######################################################
856s 
856s CPU=$(nproc || sysctl -n hw.physicalcpu)
856s 
856s ## use jellyfish
856s ${TRINITY_HOME}/Trinity --seqType fq \
856s               --max_memory 2G \
856s               --left reads.left.fq \
856s               --right reads.right.fq \
856s               --SS_lib_type RF \
856s               --CPU ${CPU} \
856s               --no_normalize_reads \
856s               --output __test_trinity_wo_normalization
856s 
856s 
856s      ______  ____   ____  ____   ____  ______  __ __
856s     |      ||    \ |    ||    \ |    ||      ||  |  |
856s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
856s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
856s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
856s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
856s       |__|  |__|\_||____||__|__||____|  |__|  |____/
856s 
856s     Trinity-v2.15.1
856s 
856s 
856s 
856s Left read files: $VAR1 = [
856s           'reads.left.fq'
856s         ];
856s Right read files: $VAR1 = [
856s           'reads.right.fq'
856s         ];
856s Monday, November 4, 2024: 14:12:02	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization
856s Monday, November 4, 2024: 14:12:02	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis
856s 
856s 
856s ----------------------------------------------------------------------------------
856s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
856s ----------------------------------------------------------------------------------
856s 
856s Converting input files. (in parallel)Monday, November 4, 2024: 14:12:02	CMD: cat /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa
856s Monday, November 4, 2024: 14:12:02	CMD: cat /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq | seqtk-trinity seq -A -R 2 - >> right.fa
856s Monday, November 4, 2024: 14:12:02	CMD: touch right.fa.ok
856s Monday, November 4, 2024: 14:12:02	CMD: touch left.fa.ok
856s Monday, November 4, 2024: 14:12:02	CMD: touch left.fa.ok right.fa.ok
856s Monday, November 4, 2024: 14:12:02	CMD: cat left.fa right.fa > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
856s Monday, November 4, 2024: 14:12:02	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa.ok
856s -------------------------------------------
856s ----------- Jellyfish  --------------------
856s -- (building a k-mer (25) catalog from reads) --
856s -------------------------------------------
856s 
856s * [Mon Nov  4 14:12:02 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
857s * [Mon Nov  4 14:12:03 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
857s * [Mon Nov  4 14:12:03 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
857s ----------------------------------------------
857s --------------- Inchworm (K=25, asm) ---------------------
857s -- (Linear contig construction from k-mers) --
857s ----------------------------------------------
857s 
857s * [Mon Nov  4 14:12:03 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa.tmp
857s Kmer length set to: 25
857s Min assembly length set to: 25
857s Monitor turned on, set to: 1
857s min entropy set to: 1
857s setting number of threads to: 2
857s -setting parallel iworm mode.
857s -reading Kmer occurrences...
858s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
858s  done parsing 520108 Kmers, 520108 added, taking 1 seconds.
858s 
858s TIMING KMER_DB_BUILDING 1 s.
858s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
858s Pruned 4291 kmers from catalog.
858s 	Pruning time: 0 seconds = 0 minutes.
858s 
858s TIMING PRUNING 0 s.
858s -populating the kmer seed candidate list.
858s Kcounter hash size: 520108
858s Processed 515817 non-zero abundance kmers in kcounter.
858s -Not sorting list of kmers, given parallel mode in effect.
858s -beginning inchworm contig assembly.
858s Total kcounter hash size: 520108 vs. sorted list size: 515817
858s num threads set to: 2
858s Done opening file. tmp.iworm.fa.pid_14790.thread_0
858s Done opening file. tmp.iworm.fa.pid_14790.thread_1
858s 
858s 	Iworm contig assembly time: 0 seconds = 0 minutes.
858s 
858s TIMING CONTIG_BUILDING 0 s.
858s 
858s TIMING PROG_RUNTIME 1 s.
858s * [Mon Nov  4 14:12:04 2024] Running CMD: mv /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa.tmp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa
858s Monday, November 4, 2024: 14:12:04	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa.finished
858s --------------------------------------------------------
858s -------------------- Chrysalis -------------------------
858s -- (Contig Clustering & de Bruijn Graph Construction) --
858s --------------------------------------------------------
858s 
858s inchworm_target: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
858s bowtie_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
858s chrysalis_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
858s * [Mon Nov  4 14:12:04 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa 100 10 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100
858s * [Mon Nov  4 14:12:04 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 1>/dev/null
859s * [Mon Nov  4 14:12:05 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm.bowtie.nameSorted.bam" 
862s * [Mon Nov  4 14:12:08 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_scaffolds.txt
862s * [Mon Nov  4 14:12:08 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt
864s * [Mon Nov  4 14:12:10 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted
864s * [Mon Nov  4 14:12:10 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
864s * [Mon Nov  4 14:12:10 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/GraphFromIwormFasta.out
864s * [Mon Nov  4 14:12:10 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/bundled_iworm_contigs.fasta -min 200
864s * [Mon Nov  4 14:12:10 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa -f /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -strand  -p 10 
866s * [Mon Nov  4 14:12:12 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/readsToComponents.out > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/readsToComponents.out.sort
866s Monday, November 4, 2024: 14:12:12	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/read_partitions/Fb_0/CBin_0
866s Monday, November 4, 2024: 14:12:12	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/partitioned_reads.files.list.ok
866s Monday, November 4, 2024: 14:12:12	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.vWCmNc/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
866s Monday, November 4, 2024: 14:12:12	CMD: touch recursive_trinity.cmds.ok
866s Monday, November 4, 2024: 14:12:12	CMD: touch recursive_trinity.cmds.ok
866s 
866s 
866s --------------------------------------------------------------------------------
866s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
866s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
866s --------------------------------------------------------------------------------
866s 
866s Monday, November 4, 2024: 14:12:12	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
866s Number of Commands: 38
925s 
succeeded(1)   2.63158% completed.    
succeeded(2)   5.26316% completed.    
succeeded(3)   7.89474% completed.    
succeeded(4)   10.5263% completed.    
succeeded(5)   13.1579% completed.    
succeeded(6)   15.7895% completed.    
succeeded(7)   18.4211% completed.    
succeeded(8)   21.0526% completed.    
succeeded(9)   23.6842% completed.    
succeeded(10)   26.3158% completed.    
succeeded(11)   28.9474% completed.    
succeeded(12)   31.5789% completed.    
succeeded(13)   34.2105% completed.    
succeeded(14)   36.8421% completed.    
succeeded(15)   39.4737% completed.    
succeeded(16)   42.1053% completed.    
succeeded(17)   44.7368% completed.    
succeeded(18)   47.3684% completed.    
succeeded(19)   50% completed.    
succeeded(20)   52.6316% completed.    
succeeded(21)   55.2632% completed.    
succeeded(22)   57.8947% completed.    
succeeded(23)   60.5263% completed.    
succeeded(24)   63.1579% completed.    
succeeded(25)   65.7895% completed.    
succeeded(26)   68.4211% completed.    
succeeded(27)   71.0526% completed.    
succeeded(28)   73.6842% completed.    
succeeded(29)   76.3158% completed.    
succeeded(30)   78.9474% completed.    
succeeded(31)   81.5789% completed.    
succeeded(32)   84.2105% completed.    
succeeded(33)   86.8421% completed.    
succeeded(34)   89.4737% completed.    
succeeded(35)   92.1053% completed.    
succeeded(36)   94.7368% completed.    
succeeded(37)   97.3684% completed.    
succeeded(38)   100% completed.    
925s 
925s All commands completed successfully. :-)
925s 
925s 
925s 
925s ** Harvesting all assembled transcripts into a single multi-fasta file...
925s 
925s Monday, November 4, 2024: 14:13:11	CMD: find /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/Trinity.tmp
925s * [Mon Nov  4 14:13:11 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa 2
927s * [Mon Nov  4 14:13:13 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta
927s Monday, November 4, 2024: 14:13:13	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta.gene_trans_map
927s 
927s 
927s #############################################################################
927s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta
927s #############################################################################
927s 
927s 
927s ./misc_run_tests/__runMe_with_qual_trimming.sh
927s 
927s 
927s 
927s #!/bin/bash -ve
927s 
927s 
927s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
927s     gunzip -c reads.right.fq.gz > reads.right.fq
927s fi
927s 
927s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
927s     gunzip -c reads.left.fq.gz > reads.left.fq
927s fi
927s 
927s 
927s 
927s #######################################################
927s ##  Run Trinity to Generate Transcriptome Assemblies ##
927s #######################################################
927s 
927s CPU=$(nproc || sysctl -n hw.physicalcpu)
927s 
927s ${TRINITY_HOME}/Trinity \
927s     --seqType fq \
927s     --max_memory 2G \
927s     --left reads.left.fq \
927s     --right reads.right.fq \
927s     --SS_lib_type RF \
927s     --CPU ${CPU} \
927s     --no_normalize_reads \
927s     --trimmomatic \
927s     --output __test_trinity_with_trimmomatic
927s 
927s 
927s      ______  ____   ____  ____   ____  ______  __ __
927s     |      ||    \ |    ||    \ |    ||      ||  |  |
927s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
927s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
927s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
927s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
927s       |__|  |__|\_||____||__|__||____|  |__|  |____/
927s 
927s     Trinity-v2.15.1
927s 
927s 
927s 
927s Left read files: $VAR1 = [
927s           'reads.left.fq'
927s         ];
927s Right read files: $VAR1 = [
927s           'reads.right.fq'
927s         ];
927s Monday, November 4, 2024: 14:13:13	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic
927s Monday, November 4, 2024: 14:13:13	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis
927s 
927s 
927s ----------------------------------------------------------------------------------
927s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
927s ----------------------------------------------------------------------------------
927s 
927s ---------------------------------------------------------------
927s ------ Quality Trimming Via Trimmomatic  ---------------------
927s << ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >>
927s ---------------------------------------------------------------
927s 
927s 
927s ## Running Trimmomatic on read files: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq, /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq
927s Monday, November 4, 2024: 14:13:13	CMD: java  -jar /usr/share/java/trimmomatic.jar PE -threads 2  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.vWCmNc/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 
927s TrimmomaticPE: Started with arguments:
927s  -threads 2 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.vWCmNc/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
927s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
927s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
927s Quality encoding detected as phred33
927s 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%)
927s TrimmomaticPE: Completed successfully
927s Monday, November 4, 2024: 14:13:13	CMD: cat reads.left.fq.P.qtrim reads.left.fq.U.qtrim > reads.left.fq.PwU.qtrim.fq
927s Monday, November 4, 2024: 14:13:13	CMD: cat reads.right.fq.P.qtrim reads.right.fq.U.qtrim > reads.right.fq.PwU.qtrim.fq
927s Monday, November 4, 2024: 14:13:13	CMD: touch trimmomatic.ok
927s Monday, November 4, 2024: 14:13:13	CMD: gzip reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim &
927s Converting input files. (in parallel)Monday, November 4, 2024: 14:13:13	CMD: cat reads.left.fq.PwU.qtrim.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa
927s Monday, November 4, 2024: 14:13:13	CMD: cat reads.right.fq.PwU.qtrim.fq | seqtk-trinity seq -A -R 2 - >> right.fa
927s Monday, November 4, 2024: 14:13:13	CMD: touch left.fa.ok
927s Monday, November 4, 2024: 14:13:13	CMD: touch right.fa.ok
927s Monday, November 4, 2024: 14:13:13	CMD: touch left.fa.ok right.fa.ok
927s Monday, November 4, 2024: 14:13:13	CMD: cat left.fa right.fa > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
927s Monday, November 4, 2024: 14:13:13	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa.ok
927s -------------------------------------------
927s ----------- Jellyfish  --------------------
927s -- (building a k-mer (25) catalog from reads) --
927s -------------------------------------------
927s 
927s * [Mon Nov  4 14:13:13 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
929s * [Mon Nov  4 14:13:15 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
929s * [Mon Nov  4 14:13:15 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
929s ----------------------------------------------
929s --------------- Inchworm (K=25, asm) ---------------------
929s -- (Linear contig construction from k-mers) --
929s ----------------------------------------------
929s 
929s * [Mon Nov  4 14:13:15 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa.tmp
929s Kmer length set to: 25
929s Min assembly length set to: 25
929s Monitor turned on, set to: 1
929s min entropy set to: 1
929s setting number of threads to: 2
929s -setting parallel iworm mode.
929s -reading Kmer occurrences...
929s 
 [0M] Kmers parsed.     
929s  done parsing 318541 Kmers, 318541 added, taking 0 seconds.
929s 
929s TIMING KMER_DB_BUILDING 0 s.
929s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
929s Pruned 1498 kmers from catalog.
929s 	Pruning time: 0 seconds = 0 minutes.
929s 
929s TIMING PRUNING 0 s.
929s -populating the kmer seed candidate list.
929s Kcounter hash size: 318541
929s Processed 317043 non-zero abundance kmers in kcounter.
929s -Not sorting list of kmers, given parallel mode in effect.
929s -beginning inchworm contig assembly.
929s Total kcounter hash size: 318541 vs. sorted list size: 317043
929s num threads set to: 2
929s Done opening file. tmp.iworm.fa.pid_21535.thread_0
929s Done opening file. tmp.iworm.fa.pid_21535.thread_1
929s 
929s 	Iworm contig assembly time: 0 seconds = 0 minutes.
929s 
929s TIMING CONTIG_BUILDING 0 s.
929s 
929s TIMING PROG_RUNTIME 0 s.
930s * [Mon Nov  4 14:13:16 2024] Running CMD: mv /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa.tmp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa
930s Monday, November 4, 2024: 14:13:16	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa.finished
930s --------------------------------------------------------
930s -------------------- Chrysalis -------------------------
930s -- (Contig Clustering & de Bruijn Graph Construction) --
930s --------------------------------------------------------
930s 
930s inchworm_target: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
930s bowtie_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
930s chrysalis_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
930s * [Mon Nov  4 14:13:16 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa 100 10 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100
930s * [Mon Nov  4 14:13:16 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 1>/dev/null
930s * [Mon Nov  4 14:13:16 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm.bowtie.nameSorted.bam" 
933s * [Mon Nov  4 14:13:19 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_scaffolds.txt
933s * [Mon Nov  4 14:13:19 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt
934s * [Mon Nov  4 14:13:20 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted
934s * [Mon Nov  4 14:13:20 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
934s * [Mon Nov  4 14:13:20 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/GraphFromIwormFasta.out
934s * [Mon Nov  4 14:13:20 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/bundled_iworm_contigs.fasta -min 200
934s * [Mon Nov  4 14:13:20 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa -f /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -strand  -p 10 
936s * [Mon Nov  4 14:13:22 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/readsToComponents.out > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/readsToComponents.out.sort
936s Monday, November 4, 2024: 14:13:22	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/read_partitions/Fb_0/CBin_0
936s Monday, November 4, 2024: 14:13:22	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/partitioned_reads.files.list.ok
936s Monday, November 4, 2024: 14:13:22	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.vWCmNc/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
936s Monday, November 4, 2024: 14:13:22	CMD: touch recursive_trinity.cmds.ok
936s Monday, November 4, 2024: 14:13:22	CMD: touch recursive_trinity.cmds.ok
936s 
936s 
936s --------------------------------------------------------------------------------
936s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
936s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
936s --------------------------------------------------------------------------------
936s 
936s Monday, November 4, 2024: 14:13:22	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
936s Number of Commands: 35
989s 
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.    
989s 
989s All commands completed successfully. :-)
989s 
989s 
989s 
989s ** Harvesting all assembled transcripts into a single multi-fasta file...
989s 
989s Monday, November 4, 2024: 14:14:15	CMD: find /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/Trinity.tmp
989s * [Mon Nov  4 14:14:15 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa 2
990s * [Mon Nov  4 14:14:16 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta
990s Monday, November 4, 2024: 14:14:16	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta.gene_trans_map
990s 
990s 
990s #############################################################################
990s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta
990s #############################################################################
990s 
990s 
990s ./misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh
990s 
990s ##### Done Running Trinity #####
990s 
990s #!/bin/bash -ve
990s 
990s 
990s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
990s     gunzip -c reads.right.fq.gz > reads.right.fq
990s fi
990s 
990s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
990s     gunzip -c reads.left.fq.gz > reads.left.fq
990s fi
990s 
990s 
990s 
990s #######################################################
990s ##  Run Trinity to Generate Transcriptome Assemblies ##
990s #######################################################
990s 
990s CPU=$(nproc || sysctl -n hw.physicalcpu)
990s 
990s ${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
990s 
990s 
990s      ______  ____   ____  ____   ____  ______  __ __
990s     |      ||    \ |    ||    \ |    ||      ||  |  |
990s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
990s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
990s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
990s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
990s       |__|  |__|\_||____||__|__||____|  |__|  |____/
990s 
990s     Trinity-v2.15.1
990s 
990s 
990s 
990s Left read files: $VAR1 = [
990s           'reads.left.fq'
990s         ];
990s Right read files: $VAR1 = [
990s           'reads.right.fq'
990s         ];
990s Monday, November 4, 2024: 14:14:16	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm
990s Monday, November 4, 2024: 14:14:16	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis
990s 
990s 
990s ----------------------------------------------------------------------------------
990s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
990s ----------------------------------------------------------------------------------
990s 
990s ---------------------------------------------------------------
990s ------ Quality Trimming Via Trimmomatic  ---------------------
990s << ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >>
990s ---------------------------------------------------------------
990s 
990s 
990s ## Running Trimmomatic on read files: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq, /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq
990s Monday, November 4, 2024: 14:14:16	CMD: java  -jar /usr/share/java/trimmomatic.jar PE -threads 2  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.vWCmNc/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 
991s TrimmomaticPE: Started with arguments:
991s  -threads 2 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.vWCmNc/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
991s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
991s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
991s Quality encoding detected as phred33
991s 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%)
991s TrimmomaticPE: Completed successfully
991s Monday, November 4, 2024: 14:14:17	CMD: cp reads.left.fq.P.qtrim reads.left.fq.PwU.qtrim.fq
991s Monday, November 4, 2024: 14:14:17	CMD: cp reads.right.fq.P.qtrim reads.right.fq.PwU.qtrim.fq
991s Monday, November 4, 2024: 14:14:17	CMD: touch trimmomatic.ok
991s Monday, November 4, 2024: 14:14:17	CMD: gzip reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim &
991s ---------------------------------------------------------------
991s ------------ In silico Read Normalization ---------------------
991s -- (Removing Excess Reads Beyond 200 Coverage --
991s ---------------------------------------------------------------
991s 
991s # running normalization on reads: $VAR1 = [
991s           [
991s             'reads.left.fq.PwU.qtrim.fq'
991s           ],
991s           [
991s             'reads.right.fq.PwU.qtrim.fq'
991s           ]
991s         ];
991s 
991s 
991s Monday, November 4, 2024: 14:14:17	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.vWCmNc/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  
991s -prepping seqs
991s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.left.fq.PwU.qtrim.fq >> left.fa
991s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.right.fq.PwU.qtrim.fq >> right.fa
991s CMD finished (0 seconds)
991s CMD finished (0 seconds)
991s CMD: touch left.fa.ok
991s CMD finished (0 seconds)
991s CMD: touch right.fa.ok
991s CMD finished (0 seconds)
991s Done converting input files.CMD: cat left.fa right.fa > both.fa
991s CMD finished (0 seconds)
991s CMD: touch both.fa.ok
991s CMD finished (0 seconds)
991s -kmer counting.
991s -------------------------------------------
991s ----------- Jellyfish  --------------------
991s -- (building a k-mer catalog from reads) --
991s -------------------------------------------
991s 
991s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
993s CMD finished (2 seconds)
993s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
993s CMD finished (0 seconds)
993s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
993s CMD finished (0 seconds)
993s CMD: touch jellyfish.K25.min2.kmers.fa.success
993s CMD finished (0 seconds)
993s -generating stats files
993s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
993s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
993s -reading Kmer occurrences...
993s -reading Kmer occurrences...
993s 
993s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
993s 
993s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
993s STATS_GENERATION_TIME: 0 seconds.
993s STATS_GENERATION_TIME: 0 seconds.
993s CMD finished (0 seconds)
993s CMD finished (0 seconds)
993s CMD: touch left.fa.K25.stats.ok
993s CMD finished (0 seconds)
993s CMD: touch right.fa.K25.stats.ok
993s CMD finished (0 seconds)
993s -sorting each stats file by read name.
993s 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
993s 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
993s CMD finished (0 seconds)
993s CMD finished (0 seconds)
993s CMD: touch left.fa.K25.stats.sort.ok
993s CMD finished (0 seconds)
993s CMD: touch right.fa.K25.stats.sort.ok
993s CMD finished (0 seconds)
993s -defining normalized reads
993s 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
993s -opening left.fa.K25.stats.sort
993s -opening right.fa.K25.stats.sort
993s -done opening files.
994s CMD finished (1 seconds)
994s CMD: touch pairs.K25.stats.ok
994s CMD finished (0 seconds)
994s 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
994s 27678 / 27726 = 99.83% reads selected during normalization.
994s 0 / 27726 = 0.00% reads discarded as likely aberrant based on coverage profiles.
994s 0 / 27726 = 0.00% reads discarded as below minimum coverage threshold=1
994s CMD finished (0 seconds)
994s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
994s CMD finished (0 seconds)
994s -search and capture.
995s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/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.
995s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.right.fq.PwU.qtrim.fq
995s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/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.
995s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.left.fq.PwU.qtrim.fq
995s CMD: touch /tmp/autopkgtest.vWCmNc/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
995s CMD finished (0 seconds)
995s CMD: touch /tmp/autopkgtest.vWCmNc/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
995s CMD finished (0 seconds)
995s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
995s CMD finished (0 seconds)
995s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
995s CMD finished (0 seconds)
995s -removing tmp dir /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/tmp_normalized_reads
995s 
995s 
995s Normalization complete. See outputs: 
995s 	/tmp/autopkgtest.vWCmNc/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
995s 	/tmp/autopkgtest.vWCmNc/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
995s Monday, November 4, 2024: 14:14:21	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/normalization.ok
995s Converting input files. (in parallel)Monday, November 4, 2024: 14:14:21	CMD: cat /tmp/autopkgtest.vWCmNc/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
995s Monday, November 4, 2024: 14:14:21	CMD: cat /tmp/autopkgtest.vWCmNc/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
995s Monday, November 4, 2024: 14:14:21	CMD: touch left.fa.ok
995s Monday, November 4, 2024: 14:14:21	CMD: touch right.fa.ok
995s Monday, November 4, 2024: 14:14:21	CMD: touch left.fa.ok right.fa.ok
995s Monday, November 4, 2024: 14:14:21	CMD: cat left.fa right.fa > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
995s Monday, November 4, 2024: 14:14:21	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa.ok
995s -------------------------------------------
995s ----------- Jellyfish  --------------------
995s -- (building a k-mer (25) catalog from reads) --
995s -------------------------------------------
995s 
995s * [Mon Nov  4 14:14:21 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
996s * [Mon Nov  4 14:14:22 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
996s * [Mon Nov  4 14:14:22 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
996s ----------------------------------------------
996s --------------- Inchworm (K=25, asm) ---------------------
996s -- (Linear contig construction from k-mers) --
996s ----------------------------------------------
996s 
996s * [Mon Nov  4 14:14:22 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa.tmp
996s Kmer length set to: 25
996s Min assembly length set to: 25
996s Monitor turned on, set to: 1
996s min entropy set to: 1
996s setting number of threads to: 2
996s -setting parallel iworm mode.
996s -reading Kmer occurrences...
996s 
 [0M] Kmers parsed.     
996s  done parsing 311705 Kmers, 311705 added, taking 0 seconds.
996s 
996s TIMING KMER_DB_BUILDING 0 s.
996s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
996s Pruned 1486 kmers from catalog.
996s 	Pruning time: 0 seconds = 0 minutes.
996s 
996s TIMING PRUNING 0 s.
996s -populating the kmer seed candidate list.
996s Kcounter hash size: 311705
996s Processed 310219 non-zero abundance kmers in kcounter.
996s -Not sorting list of kmers, given parallel mode in effect.
996s -beginning inchworm contig assembly.
996s Total kcounter hash size: 311705 vs. sorted list size: 310219
996s num threads set to: 2
996s Done opening file. tmp.iworm.fa.pid_27826.thread_0
996s Done opening file. tmp.iworm.fa.pid_27826.thread_1
997s 
997s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
997s 
997s TIMING CONTIG_BUILDING 1 s.
997s 
997s TIMING PROG_RUNTIME 1 s.
997s * [Mon Nov  4 14:14:23 2024] Running CMD: mv /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa.tmp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa
997s Monday, November 4, 2024: 14:14:23	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa.finished
997s --------------------------------------------------------
997s -------------------- Chrysalis -------------------------
997s -- (Contig Clustering & de Bruijn Graph Construction) --
997s --------------------------------------------------------
997s 
997s inchworm_target: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
997s bowtie_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
997s chrysalis_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
997s * [Mon Nov  4 14:14:23 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa 100 10 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100
997s * [Mon Nov  4 14:14:23 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 1>/dev/null
997s * [Mon Nov  4 14:14:23 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm.bowtie.nameSorted.bam" 
1000s * [Mon Nov  4 14:14:26 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_scaffolds.txt
1001s * [Mon Nov  4 14:14:27 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt
1003s * [Mon Nov  4 14:14:29 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted
1003s * [Mon Nov  4 14:14:29 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1003s * [Mon Nov  4 14:14:29 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/GraphFromIwormFasta.out
1003s * [Mon Nov  4 14:14:29 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/bundled_iworm_contigs.fasta -min 200
1003s * [Mon Nov  4 14:14:29 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa -f /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.vWCmNc/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 
1005s * [Mon Nov  4 14:14:31 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/readsToComponents.out > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/readsToComponents.out.sort
1005s Monday, November 4, 2024: 14:14:31	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/read_partitions/Fb_0/CBin_0
1005s Monday, November 4, 2024: 14:14:31	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/partitioned_reads.files.list.ok
1005s Monday, November 4, 2024: 14:14:31	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.vWCmNc/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
1005s Monday, November 4, 2024: 14:14:31	CMD: touch recursive_trinity.cmds.ok
1005s Monday, November 4, 2024: 14:14:31	CMD: touch recursive_trinity.cmds.ok
1005s 
1005s 
1005s --------------------------------------------------------------------------------
1005s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1005s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1005s --------------------------------------------------------------------------------
1005s 
1005s Monday, November 4, 2024: 14:14:31	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
1005s Number of Commands: 39
1060s 
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.    
1060s 
1060s All commands completed successfully. :-)
1060s 
1060s 
1060s 
1060s ** Harvesting all assembled transcripts into a single multi-fasta file...
1060s 
1060s Monday, November 4, 2024: 14:15:26	CMD: find /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/Trinity.tmp
1060s * [Mon Nov  4 14:15:26 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa 2
1061s * [Mon Nov  4 14:15:27 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta
1061s Monday, November 4, 2024: 14:15:27	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta.gene_trans_map
1061s 
1061s 
1061s #############################################################################
1061s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta
1061s #############################################################################
1061s 
1061s 
1061s 
1061s ##### Done Running Trinity #####
1061s 
1061s exit 0
1061s ./misc_run_tests/__test_runMe_with_jaccard_clip.sh
1061s #!/bin/bash -ve
1061s 
1061s ${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
1061s 
1061s 
1061s      ______  ____   ____  ____   ____  ______  __ __
1061s     |      ||    \ |    ||    \ |    ||      ||  |  |
1061s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1061s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1061s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1061s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1061s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1061s 
1061s     Trinity-v2.15.1
1061s 
1061s 
1061s 
1061s Left read files: $VAR1 = [
1061s           'reads.left.fq.gz'
1061s         ];
1061s Right read files: $VAR1 = [
1061s           'reads.right.fq.gz'
1061s         ];
1061s Monday, November 4, 2024: 14:15:27	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard
1061s Monday, November 4, 2024: 14:15:27	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis
1061s 
1061s 
1061s ----------------------------------------------------------------------------------
1061s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1061s ----------------------------------------------------------------------------------
1061s 
1061s ---------------------------------------------------------------
1061s ------------ In silico Read Normalization ---------------------
1061s -- (Removing Excess Reads Beyond 200 Coverage --
1061s ---------------------------------------------------------------
1061s 
1061s # running normalization on reads: $VAR1 = [
1061s           [
1061s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
1061s           ],
1061s           [
1061s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
1061s           ]
1061s         ];
1061s 
1061s 
1061s Monday, November 4, 2024: 14:15:27	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G  --max_cov 200 --min_cov 1 --CPU 1 --output /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together  --PARALLEL_STATS  
1061s -prepping seqs
1061s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
1061s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
1061s CMD finished (0 seconds)
1061s CMD finished (0 seconds)
1061s CMD: touch left.fa.ok
1061s CMD finished (0 seconds)
1061s CMD: touch right.fa.ok
1061s CMD finished (0 seconds)
1061s Done converting input files.CMD: cat left.fa right.fa > both.fa
1061s CMD finished (0 seconds)
1061s CMD: touch both.fa.ok
1061s CMD finished (0 seconds)
1061s -kmer counting.
1061s -------------------------------------------
1061s ----------- Jellyfish  --------------------
1061s -- (building a k-mer catalog from reads) --
1061s -------------------------------------------
1061s 
1061s CMD: jellyfish count -t 1 -m 25 -s 100000000  both.fa
1063s CMD finished (2 seconds)
1063s CMD: jellyfish histo -t 1 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1063s CMD finished (0 seconds)
1063s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1063s CMD finished (0 seconds)
1063s CMD: touch jellyfish.K25.min2.kmers.fa.success
1063s CMD finished (0 seconds)
1063s -generating stats files
1063s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
1063s -reading Kmer occurrences...
1063s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
1063s -reading Kmer occurrences...
1063s 
1063s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
1063s 
1063s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
1064s STATS_GENERATION_TIME: 1 seconds.
1064s CMD finished (1 seconds)
1064s STATS_GENERATION_TIME: 1 seconds.
1064s CMD finished (1 seconds)
1064s CMD: touch left.fa.K25.stats.ok
1064s CMD finished (0 seconds)
1064s CMD: touch right.fa.K25.stats.ok
1064s CMD finished (0 seconds)
1064s -sorting each stats file by read name.
1064s 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
1064s 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
1064s CMD finished (0 seconds)
1064s CMD finished (0 seconds)
1064s CMD: touch left.fa.K25.stats.sort.ok
1064s CMD finished (0 seconds)
1064s CMD: touch right.fa.K25.stats.sort.ok
1064s CMD finished (0 seconds)
1064s -defining normalized reads
1064s 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
1064s -opening left.fa.K25.stats.sort
1064s -opening right.fa.K25.stats.sort
1064s -done opening files.
1064s CMD finished (0 seconds)
1064s CMD: touch pairs.K25.stats.ok
1064s CMD finished (0 seconds)
1064s 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
1065s 30472 / 30575 = 99.66% reads selected during normalization.
1065s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1065s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
1065s CMD finished (1 seconds)
1065s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
1065s CMD finished (0 seconds)
1065s -search and capture.
1065s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture.
1065s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
1065s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture.
1065s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
1065s CMD: touch /tmp/autopkgtest.vWCmNc/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
1065s CMD finished (0 seconds)
1065s CMD: touch /tmp/autopkgtest.vWCmNc/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
1065s CMD finished (0 seconds)
1065s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1065s CMD finished (0 seconds)
1065s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1065s CMD finished (0 seconds)
1065s -removing tmp dir /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/tmp_normalized_reads
1065s 
1065s 
1065s Normalization complete. See outputs: 
1065s 	/tmp/autopkgtest.vWCmNc/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
1065s 	/tmp/autopkgtest.vWCmNc/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
1065s Monday, November 4, 2024: 14:15:31	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/normalization.ok
1065s Converting input files. (in parallel)Monday, November 4, 2024: 14:15:31	CMD: cat /tmp/autopkgtest.vWCmNc/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
1066s Monday, November 4, 2024: 14:15:32	CMD: cat /tmp/autopkgtest.vWCmNc/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
1066s Monday, November 4, 2024: 14:15:32	CMD: touch left.fa.ok
1066s Monday, November 4, 2024: 14:15:32	CMD: touch right.fa.ok
1066s Monday, November 4, 2024: 14:15:32	CMD: touch left.fa.ok right.fa.ok
1066s Monday, November 4, 2024: 14:15:32	CMD: cat left.fa right.fa > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
1066s Monday, November 4, 2024: 14:15:32	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa.ok
1066s -------------------------------------------
1066s ----------- Jellyfish  --------------------
1066s -- (building a k-mer (25) catalog from reads) --
1066s -------------------------------------------
1066s 
1066s * [Mon Nov  4 14:15:32 2024] Running CMD: jellyfish count -t 1 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
1068s * [Mon Nov  4 14:15:34 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
1068s * [Mon Nov  4 14:15:34 2024] Running CMD: jellyfish histo -t 1 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
1068s ----------------------------------------------
1068s --------------- Inchworm (K=25, asm) ---------------------
1068s -- (Linear contig construction from k-mers) --
1068s ----------------------------------------------
1068s 
1068s * [Mon Nov  4 14:15:34 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa.tmp
1068s Kmer length set to: 25
1068s Min assembly length set to: 25
1068s Monitor turned on, set to: 1
1068s min entropy set to: 1
1068s setting number of threads to: 1
1068s -setting parallel iworm mode.
1068s -reading Kmer occurrences...
1068s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
1068s  done parsing 519541 Kmers, 519541 added, taking 0 seconds.
1068s 
1068s TIMING KMER_DB_BUILDING 0 s.
1068s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
1069s Pruned 4252 kmers from catalog.
1069s 	Pruning time: 1 seconds = 0.0166667 minutes.
1069s 
1069s TIMING PRUNING 1 s.
1069s -populating the kmer seed candidate list.
1069s Kcounter hash size: 519541
1069s Processed 515289 non-zero abundance kmers in kcounter.
1069s -Not sorting list of kmers, given parallel mode in effect.
1069s -beginning inchworm contig assembly.
1069s Total kcounter hash size: 519541 vs. sorted list size: 515289
1069s num threads set to: 1
1069s Done opening file. tmp.iworm.fa.pid_34759.thread_0
1069s 
1069s 	Iworm contig assembly time: 0 seconds = 0 minutes.
1069s 
1069s TIMING CONTIG_BUILDING 0 s.
1069s 
1069s TIMING PROG_RUNTIME 1 s.
1069s * [Mon Nov  4 14:15:35 2024] Running CMD: mv /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa.tmp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa
1069s Monday, November 4, 2024: 14:15:35	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa.finished
1069s --------------------------------------------------------
1069s -------------------- Chrysalis -------------------------
1069s -- (Contig Clustering & de Bruijn Graph Construction) --
1069s --------------------------------------------------------
1069s 
1069s inchworm_target: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
1069s bowtie_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
1069s chrysalis_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
1069s * [Mon Nov  4 14:15:35 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa 100 10 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100
1069s * [Mon Nov  4 14:15:35 2024] Running CMD: /usr/bin/bowtie2-build --threads 1 -o 3 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 1>/dev/null
1070s * [Mon Nov  4 14:15:36 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm.bowtie.nameSorted.bam" 
1074s * [Mon Nov  4 14:15:40 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_scaffolds.txt
1074s * [Mon Nov  4 14:15:40 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt
1075s * [Mon Nov  4 14:15:41 2024] Running CMD: /usr/bin/sort --parallel=1 -T . -S 1G  -k9,9gr /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted
1075s * [Mon Nov  4 14:15:41 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1075s * [Mon Nov  4 14:15:41 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/GraphFromIwormFasta.out
1075s * [Mon Nov  4 14:15:41 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/bundled_iworm_contigs.fasta -min 200
1075s * [Mon Nov  4 14:15:41 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa -f /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/readsToComponents.out -t 1 -max_mem_reads 50000000  -strand  -p 10 
1078s * [Mon Nov  4 14:15:44 2024] Running CMD: /usr/bin/sort --parallel=1 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/readsToComponents.out > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/readsToComponents.out.sort
1078s Monday, November 4, 2024: 14:15:44	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0
1078s Monday, November 4, 2024: 14:15:44	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/partitioned_reads.files.list.ok
1078s Monday, November 4, 2024: 14:15:44	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.vWCmNc/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
1078s Monday, November 4, 2024: 14:15:44	CMD: touch recursive_trinity.cmds.ok
1078s Monday, November 4, 2024: 14:15:44	CMD: touch recursive_trinity.cmds.ok
1078s 
1078s 
1078s --------------------------------------------------------------------------------
1078s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1078s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1078s --------------------------------------------------------------------------------
1078s 
1078s Monday, November 4, 2024: 14:15:44	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 1 -v -shuffle 
1078s Number of Commands: 36
1079s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1079s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1079s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1079s bt2 index files: $VAR1 = [];
1079s Note - bowtie-build indices do not yet exist. Indexing genome now.
1079s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1080s CMD: touch /tmp/autopkgtest.vWCmNc/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
1080s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1080s 9900 reads; of these:
1080s   9900 (100.00%) were unpaired; of these:
1080s     5 (0.05%) aligned 0 times
1080s     5821 (58.80%) aligned exactly 1 time
1080s     4074 (41.15%) aligned >1 times
1080s 99.95% overall alignment rate
1080s CMD: touch /tmp/autopkgtest.vWCmNc/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
1080s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1081s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1081s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1081s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1081s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1081s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1081s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1081s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1081s 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
1081s 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 
1081s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1081s 
1081s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1081s 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
1081s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1081s 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
1081s 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 
1081s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1081s -processing jaccard pair sensor
1082s 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
1082s 
[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
1082s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1088s 
succeeded(1)   2.77778% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1088s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1088s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1088s bt2 index files: $VAR1 = [];
1088s Note - bowtie-build indices do not yet exist. Indexing genome now.
1088s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1088s CMD: touch /tmp/autopkgtest.vWCmNc/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
1088s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1088s 6 reads; of these:
1088s   6 (100.00%) were unpaired; of these:
1088s     0 (0.00%) aligned 0 times
1088s     6 (100.00%) aligned exactly 1 time
1088s     0 (0.00%) aligned >1 times
1088s 100.00% overall alignment rate
1088s CMD: touch /tmp/autopkgtest.vWCmNc/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
1088s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1088s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1088s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1088s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1088s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1088s 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
1088s 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 
1088s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1088s 
1088s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1088s 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
1088s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1088s 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
1088s 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 
1088s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1088s -processing jaccard pair sensor
1088s 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
1088s 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
1088s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1090s 
succeeded(2)   5.55556% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1090s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1090s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1090s bt2 index files: $VAR1 = [];
1090s Note - bowtie-build indices do not yet exist. Indexing genome now.
1090s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1090s CMD: touch /tmp/autopkgtest.vWCmNc/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
1090s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1090s 29 reads; of these:
1090s   29 (100.00%) were unpaired; of these:
1090s     0 (0.00%) aligned 0 times
1090s     29 (100.00%) aligned exactly 1 time
1090s     0 (0.00%) aligned >1 times
1090s 100.00% overall alignment rate
1090s CMD: touch /tmp/autopkgtest.vWCmNc/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
1090s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1090s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1090s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1090s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1090s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1090s 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
1090s 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 
1090s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1090s 
1090s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1090s 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
1090s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1090s 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
1090s 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 
1090s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1090s -processing jaccard pair sensor
1090s 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
1090s 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
1090s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1092s 
succeeded(3)   8.33333% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1092s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1092s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1092s bt2 index files: $VAR1 = [];
1092s Note - bowtie-build indices do not yet exist. Indexing genome now.
1092s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1092s CMD: touch /tmp/autopkgtest.vWCmNc/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
1092s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1092s 33 reads; of these:
1092s   33 (100.00%) were unpaired; of these:
1092s     0 (0.00%) aligned 0 times
1092s     33 (100.00%) aligned exactly 1 time
1092s     0 (0.00%) aligned >1 times
1092s 100.00% overall alignment rate
1092s CMD: touch /tmp/autopkgtest.vWCmNc/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
1092s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1092s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1092s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1092s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1092s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1092s 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
1092s 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 
1092s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1092s 
1092s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1092s 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
1092s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1092s 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
1092s 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 
1092s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1092s -processing jaccard pair sensor
1092s 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
1092s 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
1092s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1094s 
succeeded(4)   11.1111% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1094s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1094s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1094s bt2 index files: $VAR1 = [];
1094s Note - bowtie-build indices do not yet exist. Indexing genome now.
1094s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1094s CMD: touch /tmp/autopkgtest.vWCmNc/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
1094s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1094s 9 reads; of these:
1094s   9 (100.00%) were unpaired; of these:
1094s     0 (0.00%) aligned 0 times
1094s     9 (100.00%) aligned exactly 1 time
1094s     0 (0.00%) aligned >1 times
1094s 100.00% overall alignment rate
1094s CMD: touch /tmp/autopkgtest.vWCmNc/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
1094s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1094s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1094s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1094s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1094s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1094s 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
1094s 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 
1094s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1094s 
1094s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1094s 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
1094s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1094s 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
1094s 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 
1094s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1094s -processing jaccard pair sensor
1094s 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
1094s 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
1094s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1096s 
succeeded(5)   13.8889% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1096s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1096s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1096s bt2 index files: $VAR1 = [];
1096s Note - bowtie-build indices do not yet exist. Indexing genome now.
1096s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1096s CMD: touch /tmp/autopkgtest.vWCmNc/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
1096s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1096s 8 reads; of these:
1096s   8 (100.00%) were unpaired; of these:
1096s     0 (0.00%) aligned 0 times
1096s     8 (100.00%) aligned exactly 1 time
1096s     0 (0.00%) aligned >1 times
1096s 100.00% overall alignment rate
1096s CMD: touch /tmp/autopkgtest.vWCmNc/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
1096s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1096s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1096s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1096s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1096s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1096s 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
1096s 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 
1096s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1096s 
1096s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1096s 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
1096s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1096s 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
1096s 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 
1096s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1096s -processing jaccard pair sensor
1096s 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
1096s 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
1096s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1098s 
succeeded(6)   16.6667% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1098s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1098s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1098s bt2 index files: $VAR1 = [];
1098s Note - bowtie-build indices do not yet exist. Indexing genome now.
1098s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1098s CMD: touch /tmp/autopkgtest.vWCmNc/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
1098s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1099s 4987 reads; of these:
1099s   4987 (100.00%) were unpaired; of these:
1099s     2 (0.04%) aligned 0 times
1099s     2643 (53.00%) aligned exactly 1 time
1099s     2342 (46.96%) aligned >1 times
1099s 99.96% overall alignment rate
1099s CMD: touch /tmp/autopkgtest.vWCmNc/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
1099s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1099s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1099s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1099s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1099s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1099s 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
1099s 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 
1099s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1099s 
1099s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1099s 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
1099s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1099s 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
1099s 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 
1099s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1099s -processing jaccard pair sensor
1100s 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
1100s 
[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
1100s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1103s 
succeeded(7)   19.4444% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1103s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1103s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1103s bt2 index files: $VAR1 = [];
1103s Note - bowtie-build indices do not yet exist. Indexing genome now.
1103s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1104s CMD: touch /tmp/autopkgtest.vWCmNc/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
1104s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1104s 15 reads; of these:
1104s   15 (100.00%) were unpaired; of these:
1104s     0 (0.00%) aligned 0 times
1104s     15 (100.00%) aligned exactly 1 time
1104s     0 (0.00%) aligned >1 times
1104s 100.00% overall alignment rate
1104s CMD: touch /tmp/autopkgtest.vWCmNc/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
1104s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1104s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1104s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1104s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1104s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1104s 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
1104s 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 
1104s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1104s 
1104s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1104s 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
1104s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1104s 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
1104s 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 
1104s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1104s -processing jaccard pair sensor
1104s 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
1104s 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
1104s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1106s 
succeeded(8)   22.2222% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1106s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1106s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1106s bt2 index files: $VAR1 = [];
1106s Note - bowtie-build indices do not yet exist. Indexing genome now.
1106s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1106s CMD: touch /tmp/autopkgtest.vWCmNc/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
1106s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1106s 17 reads; of these:
1106s   17 (100.00%) were unpaired; of these:
1106s     0 (0.00%) aligned 0 times
1106s     17 (100.00%) aligned exactly 1 time
1106s     0 (0.00%) aligned >1 times
1106s 100.00% overall alignment rate
1106s CMD: touch /tmp/autopkgtest.vWCmNc/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
1106s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1106s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1106s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1106s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1106s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1106s 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
1106s 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 
1106s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1106s 
1106s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1106s 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
1106s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1106s 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
1106s 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 
1106s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1106s -processing jaccard pair sensor
1106s 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
1106s 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
1106s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1108s 
succeeded(9)   25% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1108s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1108s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1108s bt2 index files: $VAR1 = [];
1108s Note - bowtie-build indices do not yet exist. Indexing genome now.
1108s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1108s CMD: touch /tmp/autopkgtest.vWCmNc/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
1108s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1109s 7052 reads; of these:
1109s   7052 (100.00%) were unpaired; of these:
1109s     4 (0.06%) aligned 0 times
1109s     5120 (72.60%) aligned exactly 1 time
1109s     1928 (27.34%) aligned >1 times
1109s 99.94% overall alignment rate
1109s CMD: touch /tmp/autopkgtest.vWCmNc/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
1109s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1109s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1109s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1109s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1109s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1109s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1109s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1109s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1109s 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
1109s 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 
1109s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1109s 
1109s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1109s 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
1109s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1109s 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
1109s 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 
1109s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1109s -processing jaccard pair sensor
1110s 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
1110s 
[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
1110s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1120s 
succeeded(10)   27.7778% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1120s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1120s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1120s bt2 index files: $VAR1 = [];
1120s Note - bowtie-build indices do not yet exist. Indexing genome now.
1120s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1120s CMD: touch /tmp/autopkgtest.vWCmNc/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
1120s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1120s 7 reads; of these:
1120s   7 (100.00%) were unpaired; of these:
1120s     3 (42.86%) aligned 0 times
1120s     4 (57.14%) aligned exactly 1 time
1120s     0 (0.00%) aligned >1 times
1120s 57.14% overall alignment rate
1120s CMD: touch /tmp/autopkgtest.vWCmNc/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
1120s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1120s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1120s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1120s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1120s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1120s 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
1120s 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 
1120s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1120s 
1120s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1120s 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
1120s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1120s 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
1120s 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 
1120s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1120s -processing jaccard pair sensor
1120s 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
1120s 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
1120s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1121s 
succeeded(11)   30.5556% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1121s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1121s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1121s bt2 index files: $VAR1 = [];
1121s Note - bowtie-build indices do not yet exist. Indexing genome now.
1121s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1122s CMD: touch /tmp/autopkgtest.vWCmNc/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
1122s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1122s 28 reads; of these:
1122s   28 (100.00%) were unpaired; of these:
1122s     0 (0.00%) aligned 0 times
1122s     28 (100.00%) aligned exactly 1 time
1122s     0 (0.00%) aligned >1 times
1122s 100.00% overall alignment rate
1122s CMD: touch /tmp/autopkgtest.vWCmNc/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
1122s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1122s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1122s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1122s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1122s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1122s 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
1122s 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 
1122s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1122s 
1122s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1122s 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
1122s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1122s 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
1122s 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 
1122s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1122s -processing jaccard pair sensor
1122s 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
1122s 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
1122s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1124s 
succeeded(12)   33.3333% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1124s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1124s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1124s bt2 index files: $VAR1 = [];
1124s Note - bowtie-build indices do not yet exist. Indexing genome now.
1124s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1124s CMD: touch /tmp/autopkgtest.vWCmNc/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
1124s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1124s 24 reads; of these:
1124s   24 (100.00%) were unpaired; of these:
1124s     0 (0.00%) aligned 0 times
1124s     24 (100.00%) aligned exactly 1 time
1124s     0 (0.00%) aligned >1 times
1124s 100.00% overall alignment rate
1124s CMD: touch /tmp/autopkgtest.vWCmNc/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
1124s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1124s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1124s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1124s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1124s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1124s 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
1124s 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 
1124s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1124s 
1124s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1124s 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
1124s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1124s 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
1124s 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 
1124s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1124s -processing jaccard pair sensor
1124s 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
1124s 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
1124s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1126s 
succeeded(13)   36.1111% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1126s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1126s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1126s bt2 index files: $VAR1 = [];
1126s Note - bowtie-build indices do not yet exist. Indexing genome now.
1126s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1126s CMD: touch /tmp/autopkgtest.vWCmNc/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
1126s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1127s 5130 reads; of these:
1127s   5130 (100.00%) were unpaired; of these:
1127s     6 (0.12%) aligned 0 times
1127s     4306 (83.94%) aligned exactly 1 time
1127s     818 (15.95%) aligned >1 times
1127s 99.88% overall alignment rate
1127s CMD: touch /tmp/autopkgtest.vWCmNc/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
1127s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1127s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1127s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1127s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1127s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1127s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1127s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1127s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1127s 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
1127s 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 
1127s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1127s 
1127s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1127s 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
1127s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1127s 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
1127s 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 
1127s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1127s -processing jaccard pair sensor
1128s 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
1128s 
[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
1128s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1132s 
succeeded(14)   38.8889% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1132s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1132s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1132s bt2 index files: $VAR1 = [];
1132s Note - bowtie-build indices do not yet exist. Indexing genome now.
1132s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1132s CMD: touch /tmp/autopkgtest.vWCmNc/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
1132s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1133s 3374 reads; of these:
1133s   3374 (100.00%) were unpaired; of these:
1133s     1 (0.03%) aligned 0 times
1133s     2870 (85.06%) aligned exactly 1 time
1133s     503 (14.91%) aligned >1 times
1133s 99.97% overall alignment rate
1133s CMD: touch /tmp/autopkgtest.vWCmNc/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
1133s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1133s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1133s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1133s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1133s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1133s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1133s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1133s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1133s 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
1133s 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 
1133s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1133s 
1133s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1133s 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
1133s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1133s 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
1133s 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 
1133s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1133s -processing jaccard pair sensor
1133s 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
1133s 
[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
1133s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1136s 
succeeded(15)   41.6667% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1136s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1136s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1136s bt2 index files: $VAR1 = [];
1136s Note - bowtie-build indices do not yet exist. Indexing genome now.
1136s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1136s CMD: touch /tmp/autopkgtest.vWCmNc/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
1136s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1137s 6 reads; of these:
1137s   6 (100.00%) were unpaired; of these:
1137s     0 (0.00%) aligned 0 times
1137s     6 (100.00%) aligned exactly 1 time
1137s     0 (0.00%) aligned >1 times
1137s 100.00% overall alignment rate
1137s CMD: touch /tmp/autopkgtest.vWCmNc/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
1137s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1137s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1137s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1137s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1137s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1137s 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
1137s 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 
1137s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1137s 
1137s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1137s 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
1137s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1137s 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
1137s 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 
1137s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1137s -processing jaccard pair sensor
1137s 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
1137s 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
1137s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1138s 
succeeded(16)   44.4444% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1138s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1138s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1138s bt2 index files: $VAR1 = [];
1138s Note - bowtie-build indices do not yet exist. Indexing genome now.
1138s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1138s CMD: touch /tmp/autopkgtest.vWCmNc/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
1138s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1138s 8 reads; of these:
1138s   8 (100.00%) were unpaired; of these:
1138s     0 (0.00%) aligned 0 times
1138s     8 (100.00%) aligned exactly 1 time
1138s     0 (0.00%) aligned >1 times
1138s 100.00% overall alignment rate
1138s CMD: touch /tmp/autopkgtest.vWCmNc/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
1138s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1138s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1138s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1138s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1138s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1138s 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
1138s 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 
1138s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1138s 
1138s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1138s 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
1138s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1138s 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
1138s 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 
1138s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1139s -processing jaccard pair sensor
1139s 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
1139s 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
1139s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1140s 
succeeded(17)   47.2222% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1140s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1140s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1140s bt2 index files: $VAR1 = [];
1140s Note - bowtie-build indices do not yet exist. Indexing genome now.
1140s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1140s CMD: touch /tmp/autopkgtest.vWCmNc/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
1140s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1140s 14 reads; of these:
1140s   14 (100.00%) were unpaired; of these:
1140s     0 (0.00%) aligned 0 times
1140s     14 (100.00%) aligned exactly 1 time
1140s     0 (0.00%) aligned >1 times
1140s 100.00% overall alignment rate
1140s CMD: touch /tmp/autopkgtest.vWCmNc/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
1140s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1140s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1140s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1140s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1140s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1140s 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
1140s 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 
1140s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1140s 
1140s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1140s 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
1140s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1140s 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
1140s 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 
1140s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1140s -processing jaccard pair sensor
1140s 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
1140s 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
1140s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1142s 
succeeded(18)   50% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1142s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1142s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1142s bt2 index files: $VAR1 = [];
1142s Note - bowtie-build indices do not yet exist. Indexing genome now.
1142s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1142s CMD: touch /tmp/autopkgtest.vWCmNc/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
1142s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1142s 15 reads; of these:
1142s   15 (100.00%) were unpaired; of these:
1142s     0 (0.00%) aligned 0 times
1142s     15 (100.00%) aligned exactly 1 time
1142s     0 (0.00%) aligned >1 times
1142s 100.00% overall alignment rate
1142s CMD: touch /tmp/autopkgtest.vWCmNc/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
1142s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1142s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1142s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1142s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1142s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1142s 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
1142s 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 
1142s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1142s 
1142s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1142s 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
1142s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1142s 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
1142s 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 
1142s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1142s -processing jaccard pair sensor
1142s 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
1142s 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
1142s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1144s 
succeeded(19)   52.7778% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1144s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1144s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1144s bt2 index files: $VAR1 = [];
1144s Note - bowtie-build indices do not yet exist. Indexing genome now.
1144s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1144s CMD: touch /tmp/autopkgtest.vWCmNc/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
1144s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1145s 2351 reads; of these:
1145s   2351 (100.00%) were unpaired; of these:
1145s     1 (0.04%) aligned 0 times
1145s     1736 (73.84%) aligned exactly 1 time
1145s     614 (26.12%) aligned >1 times
1145s 99.96% overall alignment rate
1145s CMD: touch /tmp/autopkgtest.vWCmNc/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
1145s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1145s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1145s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1145s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1145s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1145s 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
1145s 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 
1145s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1145s 
1145s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1145s 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
1145s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1145s 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
1145s 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 
1145s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1145s -processing jaccard pair sensor
1145s 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
1145s 
[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
1145s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1149s 
succeeded(20)   55.5556% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1149s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1149s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1149s bt2 index files: $VAR1 = [];
1149s Note - bowtie-build indices do not yet exist. Indexing genome now.
1149s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1149s CMD: touch /tmp/autopkgtest.vWCmNc/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
1149s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1149s 1875 reads; of these:
1149s   1875 (100.00%) were unpaired; of these:
1149s     2 (0.11%) aligned 0 times
1149s     1543 (82.29%) aligned exactly 1 time
1149s     330 (17.60%) aligned >1 times
1149s 99.89% overall alignment rate
1149s CMD: touch /tmp/autopkgtest.vWCmNc/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
1149s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1149s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1149s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1149s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1149s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1149s 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
1149s 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 
1149s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1149s 
1149s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1149s 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
1149s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1149s 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
1149s 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 
1149s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1149s -processing jaccard pair sensor
1150s 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
1150s 
[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
1150s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1152s 
succeeded(21)   58.3333% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1152s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1152s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1152s bt2 index files: $VAR1 = [];
1152s Note - bowtie-build indices do not yet exist. Indexing genome now.
1152s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1153s CMD: touch /tmp/autopkgtest.vWCmNc/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
1153s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1153s 40 reads; of these:
1153s   40 (100.00%) were unpaired; of these:
1153s     0 (0.00%) aligned 0 times
1153s     36 (90.00%) aligned exactly 1 time
1153s     4 (10.00%) aligned >1 times
1153s 100.00% overall alignment rate
1153s CMD: touch /tmp/autopkgtest.vWCmNc/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
1153s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1153s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1153s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1153s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1153s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1153s 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
1153s 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 
1153s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1153s 
1153s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1153s 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
1153s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1153s 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
1153s 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 
1153s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1153s -processing jaccard pair sensor
1153s 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
1153s 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
1153s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1155s 
succeeded(22)   61.1111% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1155s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1155s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1155s bt2 index files: $VAR1 = [];
1155s Note - bowtie-build indices do not yet exist. Indexing genome now.
1155s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1155s CMD: touch /tmp/autopkgtest.vWCmNc/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
1155s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1155s 28 reads; of these:
1155s   28 (100.00%) were unpaired; of these:
1155s     0 (0.00%) aligned 0 times
1155s     28 (100.00%) aligned exactly 1 time
1155s     0 (0.00%) aligned >1 times
1155s 100.00% overall alignment rate
1155s CMD: touch /tmp/autopkgtest.vWCmNc/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
1155s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1155s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1155s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1155s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1155s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1155s 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
1155s 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 
1155s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1155s 
1155s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1155s 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
1155s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1155s 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
1155s 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 
1155s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1155s -processing jaccard pair sensor
1155s 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
1155s 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
1155s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1157s 
succeeded(23)   63.8889% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1157s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1157s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1157s bt2 index files: $VAR1 = [];
1157s Note - bowtie-build indices do not yet exist. Indexing genome now.
1157s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1157s CMD: touch /tmp/autopkgtest.vWCmNc/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
1157s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1157s 29 reads; of these:
1157s   29 (100.00%) were unpaired; of these:
1157s     0 (0.00%) aligned 0 times
1157s     23 (79.31%) aligned exactly 1 time
1157s     6 (20.69%) aligned >1 times
1157s 100.00% overall alignment rate
1157s CMD: touch /tmp/autopkgtest.vWCmNc/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
1157s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1157s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1157s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1157s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1157s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1157s 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
1157s 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 
1157s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1157s 
1157s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1157s 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
1157s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1157s 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
1157s 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 
1157s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1157s -processing jaccard pair sensor
1157s 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
1157s 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
1157s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1159s 
succeeded(24)   66.6667% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1159s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1159s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1159s bt2 index files: $VAR1 = [];
1159s Note - bowtie-build indices do not yet exist. Indexing genome now.
1159s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1159s CMD: touch /tmp/autopkgtest.vWCmNc/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
1159s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1159s 8 reads; of these:
1159s   8 (100.00%) were unpaired; of these:
1159s     0 (0.00%) aligned 0 times
1159s     8 (100.00%) aligned exactly 1 time
1159s     0 (0.00%) aligned >1 times
1159s 100.00% overall alignment rate
1159s CMD: touch /tmp/autopkgtest.vWCmNc/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
1159s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1159s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1159s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1159s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1159s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1159s 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
1159s 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 
1159s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1159s 
1159s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1159s 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
1159s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1159s 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
1159s 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 
1159s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1159s -processing jaccard pair sensor
1159s 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
1159s 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
1159s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1160s 
succeeded(25)   69.4444% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1160s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1160s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1160s bt2 index files: $VAR1 = [];
1160s Note - bowtie-build indices do not yet exist. Indexing genome now.
1160s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1161s CMD: touch /tmp/autopkgtest.vWCmNc/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
1161s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1161s 81 reads; of these:
1161s   81 (100.00%) were unpaired; of these:
1161s     0 (0.00%) aligned 0 times
1161s     78 (96.30%) aligned exactly 1 time
1161s     3 (3.70%) aligned >1 times
1161s 100.00% overall alignment rate
1161s CMD: touch /tmp/autopkgtest.vWCmNc/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
1161s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1161s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1161s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1161s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1161s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1161s 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
1161s 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 
1161s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1161s 
1161s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1161s 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
1161s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1161s 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
1161s 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 
1161s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1161s -processing jaccard pair sensor
1161s 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
1161s 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
1161s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1163s 
succeeded(26)   72.2222% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1163s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1163s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1163s bt2 index files: $VAR1 = [];
1163s Note - bowtie-build indices do not yet exist. Indexing genome now.
1163s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1163s CMD: touch /tmp/autopkgtest.vWCmNc/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
1163s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1163s 13 reads; of these:
1163s   13 (100.00%) were unpaired; of these:
1163s     0 (0.00%) aligned 0 times
1163s     13 (100.00%) aligned exactly 1 time
1163s     0 (0.00%) aligned >1 times
1163s 100.00% overall alignment rate
1163s CMD: touch /tmp/autopkgtest.vWCmNc/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
1163s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1163s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1163s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1163s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1163s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1163s 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
1163s 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 
1163s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1163s 
1163s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1163s 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
1163s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1163s 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
1163s 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 
1163s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1163s -processing jaccard pair sensor
1163s 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
1163s 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
1163s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1165s 
succeeded(27)   75% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1165s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1165s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1165s bt2 index files: $VAR1 = [];
1165s Note - bowtie-build indices do not yet exist. Indexing genome now.
1165s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1165s CMD: touch /tmp/autopkgtest.vWCmNc/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
1165s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1165s 1556 reads; of these:
1165s   1556 (100.00%) were unpaired; of these:
1165s     1 (0.06%) aligned 0 times
1165s     1328 (85.35%) aligned exactly 1 time
1165s     227 (14.59%) aligned >1 times
1165s 99.94% overall alignment rate
1165s CMD: touch /tmp/autopkgtest.vWCmNc/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
1165s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1165s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1165s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1165s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1165s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1165s 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
1165s 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 
1165s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1165s 
1165s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1165s 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
1165s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1165s 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
1165s 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 
1165s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1165s -processing jaccard pair sensor
1166s 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
1166s 
[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
1166s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1168s 
succeeded(28)   77.7778% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1168s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1168s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1168s bt2 index files: $VAR1 = [];
1168s Note - bowtie-build indices do not yet exist. Indexing genome now.
1168s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1168s CMD: touch /tmp/autopkgtest.vWCmNc/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
1168s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1169s 20 reads; of these:
1169s   20 (100.00%) were unpaired; of these:
1169s     0 (0.00%) aligned 0 times
1169s     20 (100.00%) aligned exactly 1 time
1169s     0 (0.00%) aligned >1 times
1169s 100.00% overall alignment rate
1169s CMD: touch /tmp/autopkgtest.vWCmNc/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
1169s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1169s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1169s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1169s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1169s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1169s 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
1169s 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 
1169s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1169s 
1169s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1169s 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
1169s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1169s 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
1169s 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 
1169s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1169s -processing jaccard pair sensor
1169s 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
1169s 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
1169s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1171s 
succeeded(29)   80.5556% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1171s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1171s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1171s bt2 index files: $VAR1 = [];
1171s Note - bowtie-build indices do not yet exist. Indexing genome now.
1171s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1171s CMD: touch /tmp/autopkgtest.vWCmNc/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
1171s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1172s 8656 reads; of these:
1172s   8656 (100.00%) were unpaired; of these:
1172s     6 (0.07%) aligned 0 times
1172s     5677 (65.58%) aligned exactly 1 time
1172s     2973 (34.35%) aligned >1 times
1172s 99.93% overall alignment rate
1172s CMD: touch /tmp/autopkgtest.vWCmNc/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
1172s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1172s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1172s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1172s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1172s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1172s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1172s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1172s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1172s 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
1172s 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 
1172s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1172s 
1172s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1172s 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
1172s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1173s 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
1173s 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 
1173s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1173s -processing jaccard pair sensor
1173s 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
1173s 
[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
1173s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1178s 
succeeded(30)   83.3333% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1178s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1178s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1178s bt2 index files: $VAR1 = [];
1178s Note - bowtie-build indices do not yet exist. Indexing genome now.
1178s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1178s CMD: touch /tmp/autopkgtest.vWCmNc/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
1178s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1178s 9 reads; of these:
1178s   9 (100.00%) were unpaired; of these:
1178s     0 (0.00%) aligned 0 times
1178s     9 (100.00%) aligned exactly 1 time
1178s     0 (0.00%) aligned >1 times
1178s 100.00% overall alignment rate
1178s CMD: touch /tmp/autopkgtest.vWCmNc/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
1178s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1178s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1178s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1178s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1178s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1178s 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
1178s 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 
1178s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1178s 
1178s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1178s 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
1178s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1178s 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
1178s 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 
1178s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1178s -processing jaccard pair sensor
1178s 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
1178s 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
1179s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1180s 
succeeded(31)   86.1111% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1180s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1180s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1180s bt2 index files: $VAR1 = [];
1180s Note - bowtie-build indices do not yet exist. Indexing genome now.
1180s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1180s CMD: touch /tmp/autopkgtest.vWCmNc/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
1180s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1180s 20 reads; of these:
1180s   20 (100.00%) were unpaired; of these:
1180s     0 (0.00%) aligned 0 times
1180s     20 (100.00%) aligned exactly 1 time
1180s     0 (0.00%) aligned >1 times
1180s 100.00% overall alignment rate
1180s CMD: touch /tmp/autopkgtest.vWCmNc/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
1180s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1180s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1180s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1180s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1180s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1180s 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
1181s 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 
1181s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1181s 
1181s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1181s 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
1181s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1181s 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
1181s 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 
1181s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1181s -processing jaccard pair sensor
1181s 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
1181s 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
1181s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1182s 
succeeded(32)   88.8889% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1182s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1182s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1182s bt2 index files: $VAR1 = [];
1182s Note - bowtie-build indices do not yet exist. Indexing genome now.
1182s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1182s CMD: touch /tmp/autopkgtest.vWCmNc/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
1182s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1183s 11 reads; of these:
1183s   11 (100.00%) were unpaired; of these:
1183s     0 (0.00%) aligned 0 times
1183s     11 (100.00%) aligned exactly 1 time
1183s     0 (0.00%) aligned >1 times
1183s 100.00% overall alignment rate
1183s CMD: touch /tmp/autopkgtest.vWCmNc/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
1183s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1183s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1183s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1183s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1183s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1183s 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
1183s 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 
1183s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1183s 
1183s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1183s 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
1183s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1183s 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
1183s 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 
1183s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1183s -processing jaccard pair sensor
1183s 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
1183s 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
1183s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1184s 
succeeded(33)   91.6667% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1184s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1184s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1184s bt2 index files: $VAR1 = [];
1184s Note - bowtie-build indices do not yet exist. Indexing genome now.
1184s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1184s CMD: touch /tmp/autopkgtest.vWCmNc/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
1184s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1184s 9 reads; of these:
1184s   9 (100.00%) were unpaired; of these:
1184s     0 (0.00%) aligned 0 times
1184s     9 (100.00%) aligned exactly 1 time
1184s     0 (0.00%) aligned >1 times
1184s 100.00% overall alignment rate
1184s CMD: touch /tmp/autopkgtest.vWCmNc/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
1184s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1184s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1184s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1184s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1184s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1184s 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
1184s 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 
1184s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1184s 
1184s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1184s 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
1184s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1184s 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
1184s 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 
1184s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1184s -processing jaccard pair sensor
1184s 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
1184s 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
1184s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1187s 
succeeded(34)   94.4444% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1187s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1187s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1187s bt2 index files: $VAR1 = [];
1187s Note - bowtie-build indices do not yet exist. Indexing genome now.
1187s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1187s CMD: touch /tmp/autopkgtest.vWCmNc/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
1187s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1189s 11272 reads; of these:
1189s   11272 (100.00%) were unpaired; of these:
1189s     2 (0.02%) aligned 0 times
1189s     1241 (11.01%) aligned exactly 1 time
1189s     10029 (88.97%) aligned >1 times
1189s 99.98% overall alignment rate
1189s CMD: touch /tmp/autopkgtest.vWCmNc/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
1189s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1189s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1190s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1190s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1190s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1190s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1190s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1190s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1190s 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
1190s 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 
1190s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1190s 
1191s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1191s 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
1191s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1191s 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
1191s 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 
1191s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1191s -processing jaccard pair sensor
1192s 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
1193s 
[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
1193s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1198s 
succeeded(35)   97.2222% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1198s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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 
1198s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/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
1198s bt2 index files: $VAR1 = [];
1198s Note - bowtie-build indices do not yet exist. Indexing genome now.
1198s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1199s CMD: touch /tmp/autopkgtest.vWCmNc/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
1199s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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" 
1199s 18 reads; of these:
1199s   18 (100.00%) were unpaired; of these:
1199s     0 (0.00%) aligned 0 times
1199s     18 (100.00%) aligned exactly 1 time
1199s     0 (0.00%) aligned >1 times
1199s 100.00% overall alignment rate
1199s CMD: touch /tmp/autopkgtest.vWCmNc/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
1199s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/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
1199s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/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
1199s CMD: samtools index /tmp/autopkgtest.vWCmNc/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
1199s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/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
1199s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1199s 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
1199s 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 
1199s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1199s 
1199s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1199s 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
1199s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1199s 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
1199s 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 
1199s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1199s -processing jaccard pair sensor
1199s 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
1199s 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
1199s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1200s 
succeeded(36)   100% completed.    
1200s 
1200s All commands completed successfully. :-)
1200s 
1200s 
1200s 
1200s ** Harvesting all assembled transcripts into a single multi-fasta file...
1200s 
1200s Monday, November 4, 2024: 14:17:46	CMD: find /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/Trinity.tmp
1200s * [Mon Nov  4 14:17:46 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa 1
1202s * [Mon Nov  4 14:17:48 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta
1202s Monday, November 4, 2024: 14:17:48	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta.gene_trans_map
1202s 
1202s 
1202s #############################################################################
1202s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta
1202s #############################################################################
1202s 
1202s 
1202s ./misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh
1202s 
1202s 
1202s exit 0
1202s #!/bin/bash -ve
1202s 
1202s 
1202s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
1202s     gunzip -c reads.right.fq.gz > reads.right.fq
1202s fi
1202s 
1202s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
1202s     gunzip -c reads.left.fq.gz > reads.left.fq
1202s fi
1202s 
1202s if [ -e reads2.right.fq.gz ] && [ ! -e reads2.right.fq ]; then
1202s     gunzip -c reads2.right.fq.gz > reads2.right.fq
1202s fi
1202s 
1202s if [ -e reads2.left.fq.gz ] && [ ! -e reads2.left.fq ]; then
1202s     gunzip -c reads2.left.fq.gz > reads2.left.fq
1202s fi
1202s 
1202s 
1202s #######################################################
1202s ##  Run Trinity to Generate Transcriptome Assemblies ##
1202s #######################################################
1202s 
1202s CPU=$(nproc || sysctl -n hw.physicalcpu)
1202s 
1202s ${TRINITY_HOME}/Trinity --seqType fq \
1202s               --max_memory 2G \
1202s               --left reads.left.fq,reads2.left.fq \
1202s               --right reads.right.fq,reads2.right.fq \
1202s               --SS_lib_type RF \
1202s               --CPU ${CPU} \
1202s               --trimmomatic \
1202s               --normalize_reads \
1202s               --normalize_by_read_set \
1202s               --output trinity_trim_and_norm_outdir
1202s 
1202s 
1202s      ______  ____   ____  ____   ____  ______  __ __
1202s     |      ||    \ |    ||    \ |    ||      ||  |  |
1202s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1202s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1202s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1202s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1202s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1202s 
1202s     Trinity-v2.15.1
1202s 
1202s 
1202s 
1202s Left read files: $VAR1 = [
1202s           'reads.left.fq',
1202s           'reads2.left.fq'
1202s         ];
1202s Right read files: $VAR1 = [
1202s           'reads.right.fq',
1202s           'reads2.right.fq'
1202s         ];
1202s Monday, November 4, 2024: 14:17:48	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir
1202s Monday, November 4, 2024: 14:17:48	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis
1202s 
1202s 
1202s ----------------------------------------------------------------------------------
1202s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1202s ----------------------------------------------------------------------------------
1202s 
1202s ---------------------------------------------------------------
1202s ------ Quality Trimming Via Trimmomatic  ---------------------
1202s << ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >>
1202s ---------------------------------------------------------------
1202s 
1202s 
1202s ## Running Trimmomatic on read files: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq, /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq
1202s Monday, November 4, 2024: 14:17:48	CMD: java  -jar /usr/share/java/trimmomatic.jar PE -threads 2  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.vWCmNc/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 
1202s TrimmomaticPE: Started with arguments:
1202s  -threads 2 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.vWCmNc/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
1202s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
1202s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
1202s Quality encoding detected as phred33
1203s 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%)
1203s TrimmomaticPE: Completed successfully
1203s Monday, November 4, 2024: 14:17:49	CMD: cp reads.left.fq.P.qtrim reads.left.fq.PwU.qtrim.fq
1203s Monday, November 4, 2024: 14:17:49	CMD: cp reads.right.fq.P.qtrim reads.right.fq.PwU.qtrim.fq
1203s Monday, November 4, 2024: 14:17:49	CMD: touch trimmomatic.ok
1203s Monday, November 4, 2024: 14:17:49	CMD: gzip reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim &
1203s 
1203s ## Running Trimmomatic on read files: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq, /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq
1203s Monday, November 4, 2024: 14:17:49	CMD: java  -jar /usr/share/java/trimmomatic.jar PE -threads 2  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq /tmp/autopkgtest.vWCmNc/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 
1203s TrimmomaticPE: Started with arguments:
1203s  -threads 2 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq /tmp/autopkgtest.vWCmNc/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
1203s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
1203s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
1203s Quality encoding detected as phred33
1204s 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%)
1204s TrimmomaticPE: Completed successfully
1204s Monday, November 4, 2024: 14:17:50	CMD: cp reads2.left.fq.P.qtrim reads2.left.fq.PwU.qtrim.fq
1204s Monday, November 4, 2024: 14:17:50	CMD: cp reads2.right.fq.P.qtrim reads2.right.fq.PwU.qtrim.fq
1204s Monday, November 4, 2024: 14:17:50	CMD: touch trimmomatic.ok
1204s Monday, November 4, 2024: 14:17:50	CMD: gzip reads2.left.fq.P.qtrim reads2.left.fq.U.qtrim reads2.right.fq.P.qtrim reads2.right.fq.U.qtrim &
1204s ---------------------------------------------------------------
1204s ------------ In silico Read Normalization ---------------------
1204s -- (Removing Excess Reads Beyond 200 Coverage --
1204s ---------------------------------------------------------------
1204s 
1204s 
1204s ## Running in silico normalization, processing each read set separately
1204s # running normalization on reads: $VAR1 = [
1204s           [
1204s             'reads.left.fq.PwU.qtrim.fq'
1204s           ],
1204s           [
1204s             'reads.right.fq.PwU.qtrim.fq'
1204s           ]
1204s         ];
1204s 
1204s 
1204s Monday, November 4, 2024: 14:17:50	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.vWCmNc/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  
1204s -prepping seqs
1204s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.left.fq.PwU.qtrim.fq >> left.fa
1204s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.right.fq.PwU.qtrim.fq >> right.fa
1204s CMD finished (0 seconds)
1204s CMD finished (0 seconds)
1204s CMD: touch left.fa.ok
1204s CMD finished (0 seconds)
1204s CMD: touch right.fa.ok
1204s CMD finished (0 seconds)
1204s Done converting input files.CMD: cat left.fa right.fa > both.fa
1204s CMD finished (0 seconds)
1204s CMD: touch both.fa.ok
1204s CMD finished (0 seconds)
1204s -kmer counting.
1204s -------------------------------------------
1204s ----------- Jellyfish  --------------------
1204s -- (building a k-mer catalog from reads) --
1204s -------------------------------------------
1204s 
1204s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
1205s CMD finished (1 seconds)
1205s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1205s CMD finished (0 seconds)
1205s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1206s CMD finished (1 seconds)
1206s CMD: touch jellyfish.K25.min2.kmers.fa.success
1206s CMD finished (0 seconds)
1206s -generating stats files
1206s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
1206s -reading Kmer occurrences...
1206s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
1206s -reading Kmer occurrences...
1206s 
1206s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
1206s 
1206s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
1206s STATS_GENERATION_TIME: 0 seconds.
1206s STATS_GENERATION_TIME: 0 seconds.
1206s CMD finished (0 seconds)
1206s CMD finished (0 seconds)
1206s CMD: touch left.fa.K25.stats.ok
1206s CMD finished (0 seconds)
1206s CMD: touch right.fa.K25.stats.ok
1206s CMD finished (0 seconds)
1206s -sorting each stats file by read name.
1206s 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
1206s 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
1206s CMD finished (0 seconds)
1206s CMD finished (0 seconds)
1206s CMD: touch left.fa.K25.stats.sort.ok
1206s CMD finished (0 seconds)
1206s CMD: touch right.fa.K25.stats.sort.ok
1206s CMD finished (0 seconds)
1206s -defining normalized reads
1206s 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
1206s -opening left.fa.K25.stats.sort
1206s -opening right.fa.K25.stats.sort
1206s -done opening files.
1206s CMD finished (0 seconds)
1206s CMD: touch pairs.K25.stats.ok
1206s CMD finished (0 seconds)
1206s 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
1207s 27678 / 27726 = 99.83% reads selected during normalization.
1207s 0 / 27726 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1207s 0 / 27726 = 0.00% reads discarded as below minimum coverage threshold=1
1207s CMD finished (1 seconds)
1207s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
1207s CMD finished (0 seconds)
1207s -search and capture.
1207s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/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.
1207s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.right.fq.PwU.qtrim.fq
1207s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/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.
1207s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.left.fq.PwU.qtrim.fq
1207s CMD: touch /tmp/autopkgtest.vWCmNc/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
1207s CMD finished (0 seconds)
1207s CMD: touch /tmp/autopkgtest.vWCmNc/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
1207s CMD finished (0 seconds)
1207s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1207s CMD finished (0 seconds)
1207s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1207s CMD finished (0 seconds)
1207s -removing tmp dir /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/tmp_normalized_reads
1207s 
1207s 
1207s Normalization complete. See outputs: 
1207s 	/tmp/autopkgtest.vWCmNc/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
1207s 	/tmp/autopkgtest.vWCmNc/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
1207s Monday, November 4, 2024: 14:17:53	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/normalization.ok
1207s # running normalization on reads: $VAR1 = [
1207s           [
1207s             'reads2.left.fq.PwU.qtrim.fq'
1207s           ],
1207s           [
1207s             'reads2.right.fq.PwU.qtrim.fq'
1207s           ]
1207s         ];
1207s 
1207s 
1207s Monday, November 4, 2024: 14:17:53	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.vWCmNc/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  
1207s -prepping seqs
1207s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.left.fq.PwU.qtrim.fq >> left.fa
1207s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.right.fq.PwU.qtrim.fq >> right.fa
1207s CMD finished (0 seconds)
1207s CMD finished (0 seconds)
1207s CMD: touch left.fa.ok
1207s CMD finished (0 seconds)
1207s CMD: touch right.fa.ok
1207s CMD finished (0 seconds)
1207s Done converting input files.CMD: cat left.fa right.fa > both.fa
1207s CMD finished (0 seconds)
1207s CMD: touch both.fa.ok
1207s CMD finished (0 seconds)
1207s -kmer counting.
1207s -------------------------------------------
1207s ----------- Jellyfish  --------------------
1207s -- (building a k-mer catalog from reads) --
1207s -------------------------------------------
1207s 
1207s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
1209s CMD finished (2 seconds)
1209s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1209s CMD finished (0 seconds)
1209s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1209s CMD finished (0 seconds)
1209s CMD: touch jellyfish.K25.min2.kmers.fa.success
1209s CMD finished (0 seconds)
1209s -generating stats files
1209s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
1209s -reading Kmer occurrences...
1209s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
1209s -reading Kmer occurrences...
1209s 
1209s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
1209s 
1209s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
1209s STATS_GENERATION_TIME: 0 seconds.
1209s CMD finished (0 seconds)
1209s STATS_GENERATION_TIME: 0 seconds.
1209s CMD finished (0 seconds)
1209s CMD: touch left.fa.K25.stats.ok
1209s CMD finished (0 seconds)
1209s CMD: touch right.fa.K25.stats.ok
1209s CMD finished (0 seconds)
1209s -sorting each stats file by read name.
1209s 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
1209s 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
1209s CMD finished (0 seconds)
1209s CMD finished (0 seconds)
1209s CMD: touch left.fa.K25.stats.sort.ok
1209s CMD finished (0 seconds)
1209s CMD: touch right.fa.K25.stats.sort.ok
1209s CMD finished (0 seconds)
1209s -defining normalized reads
1209s 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
1209s -opening left.fa.K25.stats.sort
1209s -opening right.fa.K25.stats.sort
1209s -done opening files.
1210s CMD finished (1 seconds)
1210s CMD: touch pairs.K25.stats.ok
1210s CMD finished (0 seconds)
1210s 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
1210s 27678 / 27726 = 99.83% reads selected during normalization.
1210s 0 / 27726 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1210s 0 / 27726 = 0.00% reads discarded as below minimum coverage threshold=1
1210s CMD finished (0 seconds)
1210s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
1210s CMD finished (0 seconds)
1210s -search and capture.
1211s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/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.
1211s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.left.fq.PwU.qtrim.fq
1211s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/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.
1211s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.right.fq.PwU.qtrim.fq
1211s CMD: touch /tmp/autopkgtest.vWCmNc/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
1211s CMD finished (0 seconds)
1211s CMD: touch /tmp/autopkgtest.vWCmNc/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
1211s CMD finished (0 seconds)
1211s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1211s CMD finished (0 seconds)
1211s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1211s CMD finished (0 seconds)
1211s -removing tmp dir /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/tmp_normalized_reads
1211s 
1211s 
1211s Normalization complete. See outputs: 
1211s 	/tmp/autopkgtest.vWCmNc/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
1211s 	/tmp/autopkgtest.vWCmNc/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
1211s Monday, November 4, 2024: 14:17:57	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/normalization.ok
1211s # running normalization on reads: $VAR1 = [
1211s           [
1211s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq',
1211s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq'
1211s           ],
1211s           [
1211s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq',
1211s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq'
1211s           ]
1211s         ];
1211s 
1211s 
1211s Monday, November 4, 2024: 14:17:57	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq,/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq --right /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq,/tmp/autopkgtest.vWCmNc/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  
1211s -prepping seqs
1211s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq >> left.fa
1211s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq >> right.fa
1211s CMD finished (0 seconds)
1211s CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq >> left.fa
1211s CMD finished (0 seconds)
1211s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq >> right.fa
1211s CMD finished (0 seconds)
1211s CMD finished (0 seconds)
1211s CMD: touch left.fa.ok
1211s CMD finished (0 seconds)
1211s CMD: touch right.fa.ok
1211s CMD finished (0 seconds)
1211s Done converting input files.CMD: cat left.fa right.fa > both.fa
1211s CMD finished (0 seconds)
1211s CMD: touch both.fa.ok
1211s CMD finished (0 seconds)
1211s -kmer counting.
1211s -------------------------------------------
1211s ----------- Jellyfish  --------------------
1211s -- (building a k-mer catalog from reads) --
1211s -------------------------------------------
1211s 
1211s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
1212s CMD finished (1 seconds)
1212s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1212s CMD finished (0 seconds)
1212s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1212s CMD finished (0 seconds)
1212s CMD: touch jellyfish.K25.min2.kmers.fa.success
1212s CMD finished (0 seconds)
1212s -generating stats files
1212s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
1212s -reading Kmer occurrences...
1212s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
1212s -reading Kmer occurrences...
1213s 
1213s  done parsing 311705 Kmers, 310319 added, taking 1 seconds.
1213s 
1213s  done parsing 311705 Kmers, 310319 added, taking 1 seconds.
1214s STATS_GENERATION_TIME: 1 seconds.
1214s STATS_GENERATION_TIME: 1 seconds.
1214s CMD finished (2 seconds)
1214s CMD finished (2 seconds)
1214s CMD: touch left.fa.K25.stats.ok
1214s CMD finished (0 seconds)
1214s CMD: touch right.fa.K25.stats.ok
1214s CMD finished (0 seconds)
1214s -sorting each stats file by read name.
1214s 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
1214s 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
1214s CMD finished (0 seconds)
1214s CMD finished (0 seconds)
1214s CMD: touch left.fa.K25.stats.sort.ok
1214s CMD finished (0 seconds)
1214s CMD: touch right.fa.K25.stats.sort.ok
1214s CMD finished (0 seconds)
1214s -defining normalized reads
1214s 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
1214s -opening left.fa.K25.stats.sort
1214s -opening right.fa.K25.stats.sort
1214s -done opening files.
1215s CMD finished (1 seconds)
1215s CMD: touch pairs.K25.stats.ok
1215s CMD finished (0 seconds)
1215s 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
1215s 51602 / 55356 = 93.22% reads selected during normalization.
1215s 0 / 55356 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1215s 0 / 55356 = 0.00% reads discarded as below minimum coverage threshold=1
1215s CMD finished (0 seconds)
1215s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
1215s CMD finished (0 seconds)
1215s -search and capture.
1216s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq /tmp/autopkgtest.vWCmNc/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.
1216s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq
1216s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq
1216s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq /tmp/autopkgtest.vWCmNc/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.
1216s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq
1216s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq
1216s CMD: touch /tmp/autopkgtest.vWCmNc/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
1216s CMD finished (0 seconds)
1216s CMD: touch /tmp/autopkgtest.vWCmNc/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
1216s CMD finished (0 seconds)
1216s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1216s CMD finished (0 seconds)
1216s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1216s CMD finished (0 seconds)
1216s -removing tmp dir /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/tmp_normalized_reads
1216s 
1216s 
1216s Normalization complete. See outputs: 
1216s 	/tmp/autopkgtest.vWCmNc/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
1216s 	/tmp/autopkgtest.vWCmNc/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
1216s Monday, November 4, 2024: 14:18:02	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/normalization.ok
1216s Converting input files. (in parallel)Monday, November 4, 2024: 14:18:02	CMD: cat /tmp/autopkgtest.vWCmNc/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
1216s Monday, November 4, 2024: 14:18:02	CMD: cat /tmp/autopkgtest.vWCmNc/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
1216s Monday, November 4, 2024: 14:18:02	CMD: touch right.fa.ok
1216s Monday, November 4, 2024: 14:18:02	CMD: touch left.fa.ok
1216s Monday, November 4, 2024: 14:18:02	CMD: touch left.fa.ok right.fa.ok
1216s Monday, November 4, 2024: 14:18:02	CMD: cat left.fa right.fa > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
1216s Monday, November 4, 2024: 14:18:02	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa.ok
1216s -------------------------------------------
1216s ----------- Jellyfish  --------------------
1216s -- (building a k-mer (25) catalog from reads) --
1216s -------------------------------------------
1216s 
1216s * [Mon Nov  4 14:18:02 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
1218s * [Mon Nov  4 14:18:04 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
1218s * [Mon Nov  4 14:18:04 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
1218s ----------------------------------------------
1218s --------------- Inchworm (K=25, asm) ---------------------
1218s -- (Linear contig construction from k-mers) --
1218s ----------------------------------------------
1218s 
1218s * [Mon Nov  4 14:18:04 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa.tmp
1218s Kmer length set to: 25
1218s Min assembly length set to: 25
1218s Monitor turned on, set to: 1
1218s min entropy set to: 1
1218s setting number of threads to: 2
1218s -setting parallel iworm mode.
1218s -reading Kmer occurrences...
1218s 
 [0M] Kmers parsed.     
1218s  done parsing 309493 Kmers, 309493 added, taking 0 seconds.
1218s 
1218s TIMING KMER_DB_BUILDING 0 s.
1218s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
1218s Pruned 1482 kmers from catalog.
1218s 	Pruning time: 0 seconds = 0 minutes.
1218s 
1218s TIMING PRUNING 0 s.
1218s -populating the kmer seed candidate list.
1218s Kcounter hash size: 309493
1218s Processed 308011 non-zero abundance kmers in kcounter.
1218s -Not sorting list of kmers, given parallel mode in effect.
1218s -beginning inchworm contig assembly.
1218s Total kcounter hash size: 309493 vs. sorted list size: 308011
1218s num threads set to: 2
1218s Done opening file. tmp.iworm.fa.pid_44211.thread_0
1218s Done opening file. tmp.iworm.fa.pid_44211.thread_1
1219s 
1219s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
1219s 
1219s TIMING CONTIG_BUILDING 1 s.
1219s 
1219s TIMING PROG_RUNTIME 1 s.
1219s * [Mon Nov  4 14:18:05 2024] Running CMD: mv /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa.tmp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa
1219s Monday, November 4, 2024: 14:18:05	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa.finished
1219s --------------------------------------------------------
1219s -------------------- Chrysalis -------------------------
1219s -- (Contig Clustering & de Bruijn Graph Construction) --
1219s --------------------------------------------------------
1219s 
1219s inchworm_target: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
1219s bowtie_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
1219s chrysalis_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
1219s * [Mon Nov  4 14:18:05 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa 100 10 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100
1219s * [Mon Nov  4 14:18:05 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 1>/dev/null
1219s * [Mon Nov  4 14:18:05 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm.bowtie.nameSorted.bam" 
1224s * [Mon Nov  4 14:18:10 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_scaffolds.txt
1225s * [Mon Nov  4 14:18:11 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt
1227s * [Mon Nov  4 14:18:13 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted
1227s * [Mon Nov  4 14:18:13 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1227s * [Mon Nov  4 14:18:13 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/GraphFromIwormFasta.out
1227s * [Mon Nov  4 14:18:13 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/bundled_iworm_contigs.fasta -min 200
1227s * [Mon Nov  4 14:18:13 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa -f /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.vWCmNc/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 
1230s * [Mon Nov  4 14:18:16 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/readsToComponents.out > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/readsToComponents.out.sort
1230s Monday, November 4, 2024: 14:18:16	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/read_partitions/Fb_0/CBin_0
1230s Monday, November 4, 2024: 14:18:16	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/partitioned_reads.files.list.ok
1230s Monday, November 4, 2024: 14:18:16	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.vWCmNc/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
1230s Monday, November 4, 2024: 14:18:16	CMD: touch recursive_trinity.cmds.ok
1230s Monday, November 4, 2024: 14:18:16	CMD: touch recursive_trinity.cmds.ok
1230s 
1230s 
1230s --------------------------------------------------------------------------------
1230s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1230s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1230s --------------------------------------------------------------------------------
1230s 
1230s Monday, November 4, 2024: 14:18:16	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
1230s Number of Commands: 51
1318s 
succeeded(1)   1.96078% completed.    
succeeded(2)   3.92157% completed.    
succeeded(3)   5.88235% completed.    
succeeded(4)   7.84314% completed.    
succeeded(5)   9.80392% completed.    
succeeded(6)   11.7647% completed.    
succeeded(7)   13.7255% completed.    
succeeded(8)   15.6863% completed.    
succeeded(9)   17.6471% completed.    
succeeded(10)   19.6078% completed.    
succeeded(11)   21.5686% completed.    
succeeded(12)   23.5294% completed.    
succeeded(13)   25.4902% completed.    
succeeded(14)   27.451% completed.    
succeeded(15)   29.4118% completed.    
succeeded(16)   31.3726% completed.    
succeeded(17)   33.3333% completed.    
succeeded(18)   35.2941% completed.    
succeeded(19)   37.2549% completed.    
succeeded(20)   39.2157% completed.    
succeeded(21)   41.1765% completed.    
succeeded(22)   43.1373% completed.    
succeeded(23)   45.098% completed.    
succeeded(24)   47.0588% completed.    
succeeded(25)   49.0196% completed.    
succeeded(26)   50.9804% completed.    
succeeded(27)   52.9412% completed.    
succeeded(28)   54.902% completed.    
succeeded(29)   56.8627% completed.    
succeeded(30)   58.8235% completed.    
succeeded(31)   60.7843% completed.    
succeeded(32)   62.7451% completed.    
succeeded(33)   64.7059% completed.    
succeeded(34)   66.6667% completed.    
succeeded(35)   68.6275% completed.    
succeeded(36)   70.5882% completed.    
succeeded(37)   72.549% completed.    
succeeded(38)   74.5098% completed.    
succeeded(39)   76.4706% completed.    
succeeded(40)   78.4314% completed.    
succeeded(41)   80.3922% completed.    
succeeded(42)   82.3529% completed.    
succeeded(43)   84.3137% completed.    
succeeded(44)   86.2745% completed.    
succeeded(45)   88.2353% completed.    
succeeded(46)   90.1961% completed.    
succeeded(47)   92.1569% completed.    
succeeded(48)   94.1176% completed.    
succeeded(49)   96.0784% completed.    
succeeded(50)   98.0392% completed.    
succeeded(51)   100% completed.    
1318s 
1318s All commands completed successfully. :-)
1318s 
1318s 
1318s 
1318s ** Harvesting all assembled transcripts into a single multi-fasta file...
1318s 
1318s Monday, November 4, 2024: 14:19:44	CMD: find /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/Trinity.tmp
1318s * [Mon Nov  4 14:19:44 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa 2
1319s * [Mon Nov  4 14:19:45 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta
1319s Monday, November 4, 2024: 14:19:45	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta.gene_trans_map
1319s 
1319s 
1319s #############################################################################
1319s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta
1319s #############################################################################
1319s 
1319s 
1319s ./misc_run_tests/__runMe_include_long_reads.sh
1319s 
1319s 
1319s 
1319s exit 0
1319s #!/bin/bash -ve
1319s 
1319s #######################################################
1319s ##  Run Trinity to Generate Transcriptome Assemblies ##
1319s #######################################################
1319s 
1319s CPU=$(nproc || sysctl -n hw.physicalcpu)
1319s 
1319s ${TRINITY_HOME}/Trinity --seqType fq \
1319s               --max_memory 2G \
1319s               --left reads.left.fq.gz \
1319s               --right reads.right.fq.gz \
1319s               --SS_lib_type RF \
1319s               --CPU ${CPU} \
1319s               --no_cleanup \
1319s               --long_reads longReads.fa \
1319s               --output test_trinity_long_reads
1319s 
1319s 
1319s      ______  ____   ____  ____   ____  ______  __ __
1319s     |      ||    \ |    ||    \ |    ||      ||  |  |
1319s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1319s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1319s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1319s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1319s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1319s 
1319s     Trinity-v2.15.1
1319s 
1319s 
1319s 
1319s Left read files: $VAR1 = [
1319s           'reads.left.fq.gz'
1319s         ];
1319s Right read files: $VAR1 = [
1319s           'reads.right.fq.gz'
1319s         ];
1319s Monday, November 4, 2024: 14:19:45	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads
1319s Monday, November 4, 2024: 14:19:45	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis
1319s 
1319s 
1319s ----------------------------------------------------------------------------------
1319s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1319s ----------------------------------------------------------------------------------
1319s 
1319s ---------------------------------------------------------------
1319s ------------ In silico Read Normalization ---------------------
1319s -- (Removing Excess Reads Beyond 200 Coverage --
1319s ---------------------------------------------------------------
1319s 
1319s # running normalization on reads: $VAR1 = [
1319s           [
1319s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
1319s           ],
1319s           [
1319s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
1319s           ]
1319s         ];
1319s 
1319s 
1319s Monday, November 4, 2024: 14:19:45	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together  --PARALLEL_STATS  
1319s -prepping seqs
1319s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
1319s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
1319s CMD finished (0 seconds)
1319s CMD finished (0 seconds)
1319s CMD: touch left.fa.ok
1319s CMD finished (0 seconds)
1319s CMD: touch right.fa.ok
1319s CMD finished (0 seconds)
1319s Done converting input files.CMD: cat left.fa right.fa > both.fa
1319s CMD finished (0 seconds)
1319s CMD: touch both.fa.ok
1319s CMD finished (0 seconds)
1319s -kmer counting.
1319s -------------------------------------------
1319s ----------- Jellyfish  --------------------
1319s -- (building a k-mer catalog from reads) --
1319s -------------------------------------------
1319s 
1319s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
1321s CMD finished (2 seconds)
1321s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1321s CMD finished (0 seconds)
1321s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1321s CMD finished (0 seconds)
1321s CMD: touch jellyfish.K25.min2.kmers.fa.success
1321s CMD finished (0 seconds)
1321s -generating stats files
1321s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
1321s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
1321s -reading Kmer occurrences...
1321s -reading Kmer occurrences...
1321s 
1321s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
1321s 
1321s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
1321s STATS_GENERATION_TIME: 0 seconds.
1321s CMD finished (0 seconds)
1321s STATS_GENERATION_TIME: 0 seconds.
1321s CMD finished (0 seconds)
1321s CMD: touch left.fa.K25.stats.ok
1321s CMD finished (0 seconds)
1321s CMD: touch right.fa.K25.stats.ok
1321s CMD finished (0 seconds)
1321s -sorting each stats file by read name.
1321s 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
1321s 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
1321s CMD finished (0 seconds)
1321s CMD finished (0 seconds)
1321s CMD: touch left.fa.K25.stats.sort.ok
1321s CMD finished (0 seconds)
1321s CMD: touch right.fa.K25.stats.sort.ok
1321s CMD finished (0 seconds)
1321s -defining normalized reads
1321s 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
1321s -opening left.fa.K25.stats.sort
1321s -opening right.fa.K25.stats.sort
1321s -done opening files.
1322s CMD finished (1 seconds)
1322s CMD: touch pairs.K25.stats.ok
1322s CMD finished (0 seconds)
1322s 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
1322s 30472 / 30575 = 99.66% reads selected during normalization.
1322s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1322s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
1322s CMD finished (0 seconds)
1322s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
1322s CMD finished (0 seconds)
1322s -search and capture.
1322s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture.
1322s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
1322s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture.
1322s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
1323s CMD: touch /tmp/autopkgtest.vWCmNc/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
1323s CMD finished (0 seconds)
1323s CMD: touch /tmp/autopkgtest.vWCmNc/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
1323s CMD finished (0 seconds)
1323s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1323s CMD finished (0 seconds)
1323s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1323s CMD finished (0 seconds)
1323s 
1323s 
1323s Normalization complete. See outputs: 
1323s 	/tmp/autopkgtest.vWCmNc/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
1323s 	/tmp/autopkgtest.vWCmNc/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
1323s Monday, November 4, 2024: 14:19:49	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/normalization.ok
1323s Converting input files. (in parallel)Monday, November 4, 2024: 14:19:49	CMD: cat /tmp/autopkgtest.vWCmNc/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
1323s Monday, November 4, 2024: 14:19:49	CMD: cat /tmp/autopkgtest.vWCmNc/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
1323s Monday, November 4, 2024: 14:19:49	CMD: touch left.fa.ok
1323s Monday, November 4, 2024: 14:19:49	CMD: touch right.fa.ok
1323s Monday, November 4, 2024: 14:19:49	CMD: touch left.fa.ok right.fa.ok
1323s Monday, November 4, 2024: 14:19:49	CMD: cat left.fa right.fa > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa
1323s Monday, November 4, 2024: 14:19:49	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.ok
1323s Monday, November 4, 2024: 14:19:49	CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR
1323s Monday, November 4, 2024: 14:19:49	CMD: cat /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/longReads.fa | sed 's/>/>LR\$\|/' >> /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR
1323s Monday, November 4, 2024: 14:19:49	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR.ok
1323s -------------------------------------------
1323s ----------- Jellyfish  --------------------
1323s -- (building a k-mer (25) catalog from reads) --
1323s -------------------------------------------
1323s 
1323s * [Mon Nov  4 14:19:49 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa
1324s * [Mon Nov  4 14:19:50 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
1324s * [Mon Nov  4 14:19:50 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
1324s ----------------------------------------------
1324s --------------- Inchworm (K=25, asm) ---------------------
1324s -- (Linear contig construction from k-mers) --
1324s ----------------------------------------------
1324s 
1324s * [Mon Nov  4 14:19:50 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa.tmp
1324s Kmer length set to: 25
1324s Min assembly length set to: 25
1324s Monitor turned on, set to: 1
1324s -retaining tmp files
1324s min entropy set to: 1
1324s setting number of threads to: 2
1324s -setting parallel iworm mode.
1324s -reading Kmer occurrences...
1325s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
1325s  done parsing 519541 Kmers, 519541 added, taking 1 seconds.
1325s 
1325s TIMING KMER_DB_BUILDING 1 s.
1325s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
1325s Pruned 4252 kmers from catalog.
1325s 	Pruning time: 0 seconds = 0 minutes.
1325s 
1325s TIMING PRUNING 0 s.
1325s -populating the kmer seed candidate list.
1325s Kcounter hash size: 519541
1325s Processed 515289 non-zero abundance kmers in kcounter.
1325s -Not sorting list of kmers, given parallel mode in effect.
1325s -beginning inchworm contig assembly.
1325s Total kcounter hash size: 519541 vs. sorted list size: 515289
1325s num threads set to: 2
1325s Done opening file. tmp.iworm.fa.pid_53148.thread_0
1325s Done opening file. tmp.iworm.fa.pid_53148.thread_1
1326s 
1326s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
1326s 
1326s TIMING CONTIG_BUILDING 1 s.
1326s 
1326s TIMING PROG_RUNTIME 2 s.
1326s * [Mon Nov  4 14:19:52 2024] Running CMD: mv /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa.tmp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa
1326s Monday, November 4, 2024: 14:19:52	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa.finished
1326s --------------------------------------------------------
1326s -------------------- Chrysalis -------------------------
1326s -- (Contig Clustering & de Bruijn Graph Construction) --
1326s --------------------------------------------------------
1326s 
1326s inchworm_target: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa
1326s bowtie_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa
1326s chrysalis_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR
1326s * [Mon Nov  4 14:19:52 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa 100 10 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100
1326s * [Mon Nov  4 14:19:52 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 1>/dev/null
1326s * [Mon Nov  4 14:19:52 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm.bowtie.nameSorted.bam" 
1329s * [Mon Nov  4 14:19:55 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_scaffolds.txt
1330s * [Mon Nov  4 14:19:56 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt
1333s * [Mon Nov  4 14:19:59 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted
1333s * [Mon Nov  4 14:19:59 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1333s * [Mon Nov  4 14:19:59 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/GraphFromIwormFasta.out
1333s * [Mon Nov  4 14:19:59 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/bundled_iworm_contigs.fasta -min 200
1333s * [Mon Nov  4 14:19:59 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR -f /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -strand  -p 10 
1335s * [Mon Nov  4 14:20:01 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/readsToComponents.out > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/readsToComponents.out.sort
1335s Monday, November 4, 2024: 14:20:01	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/read_partitions/Fb_0/CBin_0
1335s Monday, November 4, 2024: 14:20:01	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/partitioned_reads.files.list.ok
1335s Monday, November 4, 2024: 14:20:01	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.vWCmNc/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
1335s Monday, November 4, 2024: 14:20:01	CMD: touch recursive_trinity.cmds.ok
1335s Monday, November 4, 2024: 14:20:01	CMD: touch recursive_trinity.cmds.ok
1335s 
1335s 
1335s --------------------------------------------------------------------------------
1335s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1335s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1335s --------------------------------------------------------------------------------
1335s 
1335s Monday, November 4, 2024: 14:20:01	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
1335s Number of Commands: 41
1393s 
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.    
1393s 
1393s All commands completed successfully. :-)
1393s 
1393s 
1393s 
1393s ** Harvesting all assembled transcripts into a single multi-fasta file...
1393s 
1393s Monday, November 4, 2024: 14:20:59	CMD: find /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/Trinity.tmp
1393s * [Mon Nov  4 14:20:59 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa 2
1394s * [Mon Nov  4 14:21:00 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta
1394s Monday, November 4, 2024: 14:21:00	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta.gene_trans_map
1394s 
1394s 
1394s #############################################################################
1394s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta
1394s #############################################################################
1394s 
1394s 
1394s 
1394s 
1394s find test_trinity_long_reads/ -regex ".*allProbPaths.fasta"  -exec cat {} \; | grep LR
1394s >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(+)]}
1394s >c0_g2_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$|mm9chr8-NM_027590;mm9chr8-70885_Ints10_integrator_complex_subunit_10_mm9chr8:71317919-71351332(+)]}
1394s >c0_g2_i16 len=2273 path=[1:0-1204 1183:1205-1226 1205:1227-1649 1628:1650-1650 6231:1651-1674 1653:1675-2040 2019:2041-2041 2020:2042-2063 2042:2064-2227 2206:2228-2248 6207:2249-2272] [-1, 1, 1183, 1205, 1628, 6231, 1653, 2019, 2020, 2042, 2206, 6207, -2] long_read_mappings: {PairPath [_paths=[[1, 1183, 1205, 1628, 6231, 1653, 2019, 2020, 2042], []]]=[LR$|mm9chr8-NM_027590;mm9chr8-70885_Ints10_integrator_complex_subunit_10_mm9chr8:71317919-71351332(+)]}
1394s >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$|mm9chr4-NM_010598;mm9chr4-16498_Kcnab2_potassium_voltage-gated_channel,_shaker-related_mm9chr4:151767144-151809990(-)]}
1394s >c0_g1_i3 len=3590 path=[3675:0-117 3770:118-137 265:138-140 268:141-250 3806:251-310 396:311-3589] [-1, 3675, 3770, 265, 268, 3806, 396, -2] long_read_mappings: {PairPath [_paths=[[268, 3806, 396], []]]=[LR$|mm9chr4-NM_010598;mm9chr4-16498_Kcnab2_potassium_voltage-gated_channel,_shaker-related_mm9chr4:151767144-151809990(-)]}
1394s >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$|mm9chr6-NM_022332;mm9chr6-64213_St7_low_density_lipoprotein-related_protein_12_mm9chr6:17699593-17892765(+)]}
1394s >c0_g1_i5 len=2364 path=[1:0-610 589:611-1077 1056:1078-1099 1078:1100-1541 1520:1542-1621 1600:1622-1794 1773:1795-2028 2007:2029-2029 2008:2030-2363] [-1, 1, 589, 1056, 1078, 1520, 1600, 1773, 2007, 2008, -2] long_read_mappings: {PairPath [_paths=[[1, 589, 1056, 1078, 1520, 1600, 1773, 2007, 2008], []]]=[LR$|mm9chr6-NM_001083315;mm9chr6-64213_St7_low_density_lipoprotein-related_protein_12_mm9chr6:17699593-17892765(+)]}
1394s >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$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]}
1394s >c0_g1_i2 len=2177 path=[2641:0-65 2684:66-412 3031:413-413 3032:414-495 3114:496-2156 8302:2157-2176] [-1, 2641, 2684, 3031, 3032, 3114, 8302, -2] long_read_mappings: {PairPath [_paths=[[3114], []]]=[LR$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]}
1394s >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$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]}
1394s >c0_g1_i4 len=5494 path=[2641:0-65 2684:66-412 3031:413-413 3032:414-495 3114:496-2156 4775:2157-3903 6522:3904-3919 6538:3920-4997 7616:4998-4998 7617:4999-5035 7616:5036-5036 7654:5037-5493] [-1, 2641, 2684, 3031, 3032, 3114, 4775, 6522, 6538, 7616, 7617, 7616, 7654, -2] long_read_mappings: {PairPath [_paths=[[3114], []]]=[LR$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]}
1394s >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$|mm9chr2-NM_033134;mm9chr2-64436_Inpp5e_inositol_polyphosphate-5-phosphatase_E_mm9chr2:26253359-26264107(-)]}
1394s >c0_g3_i2 len=3966 path=[5835:0-165 147:166-1345 5978:1346-1417 1348:1418-1418 7191:1419-1442 1373:1443-1489 1420:1490-1490 1421:1491-1650 1581:1651-2963 2894:2964-3730 6074:3731-3965] [-1, 5835, 147, 5978, 1348, 7191, 1373, 1420, 1421, 1581, 2894, 6074, -2] long_read_mappings: {PairPath [_paths=[[147, 5978, 1348, 7191, 1373, 1420, 1421, 1581, 2894, 6074], []]]=[LR$|mm9chr7-NM_022979;mm9chr7-269966_Nup98_nucleoporin_98_mm9chr7:109283074-109344374(-)]}
1394s >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$|mm9chr1-NM_001102430;mm9chr1-211673_Arfgef1_ADP-ribosylation_factor_guanine_mm9chr1:10128913-10222575(-)]}
1394s >c0_g1_i2 len=6219 path=[1:0-1805 1784:1806-1822 1801:1823-5597 5576:5598-5738 5717:5739-5739 5718:5740-6173 7351:6174-6177 7355:6178-6178 7445:6179-6218] [-1, 1, 1784, 1801, 5576, 5717, 5718, 7351, 7355, 7445, -2] long_read_mappings: {PairPath [_paths=[[1, 1784, 1801, 5576, 5717, 5718], []]]=[LR$|mm9chr1-NM_001102430;mm9chr1-211673_Arfgef1_ADP-ribosylation_factor_guanine_mm9chr1:10128913-10222575(-)]}
1394s >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$|mm9chr1-NM_001102430;mm9chr1-211673_Arfgef1_ADP-ribosylation_factor_guanine_mm9chr1:10128913-10222575(-)]}
1394s >c0_g3_i6 len=7669 path=[1:0-333 312:334-1874 1853:1875-2722 2701:2723-3436 3415:3437-3734 10929:3735-3758 3737:3759-3759 3738:3760-4380 4359:4381-6314 6293:6315-6645 6624:6646-6646 6625:6647-6661 6640:6662-6662 6641:6663-7161 7140:7162-7164 7143:7165-7182 7161:7183-7208 7187:7209-7239 7218:7240-7260 7239:7261-7261 10928:7262-7285 7264:7286-7623 8735:7624-7668] [-1, 1, 312, 1853, 2701, 3415, 10929, 3737, 3738, 4359, 6293, 6624, 6625, 6640, 6641, 7140, 7143, 7161, 7187, 7218, 7239, 10928, 7264, 8735, -2] long_read_mappings: {PairPath [_paths=[[1, 312, 1853, 2701, 3415, 10929, 3737, 3738, 4359, 6293, 6624, 6625, 6640, 6641, 7140, 7143, 7161, 7187, 7218, 7239, 10928, 7264], []]]=[LR$|mm9chr2-NM_153125;mm9chr2-227648_Sec16a_SEC16_homolog_A_mm9chr2:26266405-26297521(-)]}
1394s >c0_g3_i8 len=8757 path=[1:0-333 312:334-1874 1853:1875-2722 2701:2723-3436 3415:3437-3734 10929:3735-3758 3737:3759-3759 3738:3760-4380 4359:4381-6314 6293:6315-6645 6624:6646-6646 6625:6647-6661 6640:6662-6662 6641:6663-7161 7140:7162-7164 7143:7165-7182 7161:7183-7208 7187:7209-7239 7218:7240-7260 7239:7261-7261 10928:7262-7285 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, 10929, 3737, 3738, 4359, 6293, 6624, 6625, 6640, 6641, 7140, 7143, 7161, 7187, 7218, 7239, 10928, 7264, 7602, 7947, 7948, 7961, 7962, 8231, 8726, -2] long_read_mappings: {PairPath [_paths=[[1, 312, 1853, 2701, 3415, 10929, 3737, 3738, 4359, 6293, 6624, 6625, 6640, 6641, 7140, 7143, 7161, 7187, 7218, 7239, 10928, 7264], []]]=[LR$|mm9chr2-NM_153125;mm9chr2-227648_Sec16a_SEC16_homolog_A_mm9chr2:26266405-26297521(-)]}
1394s >c0_g1_i2 len=4179 path=[1:0-1751 1730:1752-1773 1752:1774-2693 2672:2694-4164 5684:4165-4178] [-1, 1, 1730, 1752, 2672, 5684, -2] long_read_mappings: {PairPath [_paths=[[1, 1730, 1752, 2672], []]]=[LR$|mm9chr5-NM_172722;mm9chr5-231713_Naa25_Nalpha_acteyltransferase_25_mm9chr5:121848014-121889959(+)]}
1394s >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(+)]}
1394s 
1394s 
1394s exit 0
1394s ./misc_run_tests/__run_PE_samples_file.sh
1394s #!/bin/bash -ve
1394s 
1394s ${TRINITY_HOME}/Trinity --samples_file samples.PE.txt \
1394s               --seqType fq \
1394s               --max_memory 1G \
1394s               --output trinity_test_samples_PE
1394s 
1394s 
1394s      ______  ____   ____  ____   ____  ______  __ __
1394s     |      ||    \ |    ||    \ |    ||      ||  |  |
1394s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1394s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1394s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1394s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1394s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1394s 
1394s     Trinity-v2.15.1
1394s 
1394s 
1394s 
1394s Left read files: $VAR1 = [
1394s           'reads.left.fq.gz',
1394s           'reads2.left.fq.gz'
1394s         ];
1394s Right read files: $VAR1 = [
1394s           'reads.right.fq.gz',
1394s           'reads2.right.fq.gz'
1394s         ];
1394s Monday, November 4, 2024: 14:21:00	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE
1394s Monday, November 4, 2024: 14:21:00	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis
1394s 
1394s 
1394s ----------------------------------------------------------------------------------
1394s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1394s ----------------------------------------------------------------------------------
1394s 
1394s ---------------------------------------------------------------
1394s ------------ In silico Read Normalization ---------------------
1394s -- (Removing Excess Reads Beyond 200 Coverage --
1394s ---------------------------------------------------------------
1394s 
1394s # running normalization on reads: $VAR1 = [
1394s           [
1394s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz',
1394s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz'
1394s           ],
1394s           [
1394s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz',
1394s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz'
1394s           ]
1394s         ];
1394s 
1394s 
1394s Monday, November 4, 2024: 14:21:00	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization --max_CV 10000  --left /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz --right /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz,/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz --pairs_together  --PARALLEL_STATS  
1394s -prepping seqs
1394s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
1394s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
1395s CMD finished (1 seconds)
1395s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz) >> left.fa
1395s CMD finished (1 seconds)
1395s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz) >> right.fa
1395s CMD finished (0 seconds)
1395s CMD finished (0 seconds)
1395s CMD: touch left.fa.ok
1395s CMD finished (0 seconds)
1395s CMD: touch right.fa.ok
1395s CMD finished (0 seconds)
1395s Done converting input files.CMD: cat left.fa right.fa > both.fa
1395s CMD finished (0 seconds)
1395s CMD: touch both.fa.ok
1395s CMD finished (0 seconds)
1395s -kmer counting.
1395s -------------------------------------------
1395s ----------- Jellyfish  --------------------
1395s -- (building a k-mer catalog from reads) --
1395s -------------------------------------------
1395s 
1395s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  both.fa
1396s CMD finished (1 seconds)
1396s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1396s CMD finished (0 seconds)
1396s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1396s CMD finished (0 seconds)
1396s CMD: touch jellyfish.K25.min2.kmers.fa.success
1396s CMD finished (0 seconds)
1396s -generating stats files
1396s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > left.fa.K25.stats
1396s -reading Kmer occurrences...
1396s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > right.fa.K25.stats
1396s -reading Kmer occurrences...
1397s 
1397s  done parsing 518514 Kmers, 518514 added, taking 1 seconds.
1397s 
1397s  done parsing 518514 Kmers, 518514 added, taking 1 seconds.
1398s STATS_GENERATION_TIME: 1 seconds.
1398s STATS_GENERATION_TIME: 1 seconds.
1398s CMD finished (2 seconds)
1398s CMD finished (2 seconds)
1398s CMD: touch left.fa.K25.stats.ok
1398s CMD finished (0 seconds)
1398s CMD: touch right.fa.K25.stats.ok
1398s CMD finished (0 seconds)
1398s -sorting each stats file by read name.
1398s 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
1398s 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
1398s CMD finished (0 seconds)
1398s CMD finished (0 seconds)
1398s CMD: touch left.fa.K25.stats.sort.ok
1398s CMD finished (0 seconds)
1398s CMD: touch right.fa.K25.stats.sort.ok
1398s CMD finished (0 seconds)
1398s -defining normalized reads
1398s 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
1398s -opening left.fa.K25.stats.sort
1398s -opening right.fa.K25.stats.sort
1398s -done opening files.
1399s CMD finished (1 seconds)
1399s CMD: touch pairs.K25.stats.ok
1399s CMD finished (0 seconds)
1399s 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
1400s 56508 / 61150 = 92.41% reads selected during normalization.
1400s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1400s 0 / 61150 = 0.00% reads discarded as below minimum coverage threshold=1
1400s CMD finished (1 seconds)
1400s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
1400s CMD finished (0 seconds)
1400s -search and capture.
1400s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz ... done prepping, now search and capture.
1400s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
1400s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz ... done prepping, now search and capture.
1400s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
1400s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz
1400s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz
1401s CMD: touch /tmp/autopkgtest.vWCmNc/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
1401s CMD finished (0 seconds)
1401s CMD: touch /tmp/autopkgtest.vWCmNc/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
1401s CMD finished (0 seconds)
1401s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1401s CMD finished (0 seconds)
1401s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1401s CMD finished (0 seconds)
1401s -removing tmp dir /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/tmp_normalized_reads
1401s 
1401s 
1401s Normalization complete. See outputs: 
1401s 	/tmp/autopkgtest.vWCmNc/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
1401s 	/tmp/autopkgtest.vWCmNc/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
1401s Monday, November 4, 2024: 14:21:07	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/normalization.ok
1401s Converting input files. (in parallel)Monday, November 4, 2024: 14:21:07	CMD: cat /tmp/autopkgtest.vWCmNc/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
1401s Monday, November 4, 2024: 14:21:07	CMD: cat /tmp/autopkgtest.vWCmNc/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
1401s Monday, November 4, 2024: 14:21:07	CMD: touch left.fa.ok
1401s Monday, November 4, 2024: 14:21:07	CMD: touch right.fa.ok
1401s Monday, November 4, 2024: 14:21:07	CMD: touch left.fa.ok right.fa.ok
1401s Monday, November 4, 2024: 14:21:07	CMD: cat left.fa right.fa > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
1401s Monday, November 4, 2024: 14:21:07	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa.ok
1401s -------------------------------------------
1401s ----------- Jellyfish  --------------------
1401s -- (building a k-mer (25) catalog from reads) --
1401s -------------------------------------------
1401s 
1401s * [Mon Nov  4 14:21:07 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
1403s * [Mon Nov  4 14:21:09 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
1403s * [Mon Nov  4 14:21:09 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
1403s ----------------------------------------------
1403s --------------- Inchworm (K=25, asm) ---------------------
1403s -- (Linear contig construction from k-mers) --
1403s ----------------------------------------------
1403s 
1403s * [Mon Nov  4 14:21:09 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa.tmp
1403s Kmer length set to: 25
1403s Min assembly length set to: 25
1403s Monitor turned on, set to: 1
1403s double stranded mode set
1403s min entropy set to: 1
1403s setting number of threads to: 2
1403s -setting parallel iworm mode.
1403s -reading Kmer occurrences...
1404s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
1404s  done parsing 515206 Kmers, 515206 added, taking 0 seconds.
1404s 
1404s TIMING KMER_DB_BUILDING 0 s.
1404s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
1404s Pruned 4139 kmers from catalog.
1404s 	Pruning time: 1 seconds = 0.0166667 minutes.
1404s 
1404s TIMING PRUNING 1 s.
1404s -populating the kmer seed candidate list.
1404s Kcounter hash size: 515206
1404s Processed 511067 non-zero abundance kmers in kcounter.
1404s -Not sorting list of kmers, given parallel mode in effect.
1404s -beginning inchworm contig assembly.
1404s Total kcounter hash size: 515206 vs. sorted list size: 511067
1404s num threads set to: 2
1404s Done opening file. tmp.iworm.fa.pid_60644.thread_0
1404s Done opening file. tmp.iworm.fa.pid_60644.thread_1
1405s 
1405s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
1405s 
1405s TIMING CONTIG_BUILDING 1 s.
1405s 
1405s TIMING PROG_RUNTIME 2 s.
1405s * [Mon Nov  4 14:21:11 2024] Running CMD: mv /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa.tmp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa
1405s Monday, November 4, 2024: 14:21:11	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa.finished
1405s --------------------------------------------------------
1405s -------------------- Chrysalis -------------------------
1405s -- (Contig Clustering & de Bruijn Graph Construction) --
1405s --------------------------------------------------------
1405s 
1405s inchworm_target: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
1405s bowtie_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
1405s chrysalis_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
1405s * [Mon Nov  4 14:21:11 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa 100 10 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100
1405s * [Mon Nov  4 14:21:11 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 1>/dev/null
1405s * [Mon Nov  4 14:21:11 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm.bowtie.nameSorted.bam" 
1414s * [Mon Nov  4 14:21:20 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_scaffolds.txt
1415s * [Mon Nov  4 14:21:21 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt
1417s * [Mon Nov  4 14:21:23 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G  -k9,9gr /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted
1417s * [Mon Nov  4 14:21:23 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1417s * [Mon Nov  4 14:21:23 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100  -weld_graph /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/GraphFromIwormFasta.out
1417s * [Mon Nov  4 14:21:23 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/bundled_iworm_contigs.fasta -min 200
1417s * [Mon Nov  4 14:21:23 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa -f /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -p 10 
1423s * [Mon Nov  4 14:21:29 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/readsToComponents.out > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/readsToComponents.out.sort
1423s Monday, November 4, 2024: 14:21:29	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/read_partitions/Fb_0/CBin_0
1423s Monday, November 4, 2024: 14:21:29	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/partitioned_reads.files.list.ok
1423s Monday, November 4, 2024: 14:21:29	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.vWCmNc/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
1423s Monday, November 4, 2024: 14:21:29	CMD: touch recursive_trinity.cmds.ok
1423s Monday, November 4, 2024: 14:21:29	CMD: touch recursive_trinity.cmds.ok
1423s 
1423s 
1423s --------------------------------------------------------------------------------
1423s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1423s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1423s --------------------------------------------------------------------------------
1423s 
1423s Monday, November 4, 2024: 14:21:29	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
1423s Number of Commands: 61
1531s 
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.    
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succeeded(11)   18.0328% completed.    
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succeeded(23)   37.7049% completed.    
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succeeded(25)   40.9836% completed.    
succeeded(26)   42.623% completed.    
succeeded(27)   44.2623% completed.    
succeeded(28)   45.9016% completed.    
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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.    
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succeeded(36)   59.0164% completed.    
succeeded(37)   60.6557% completed.    
succeeded(38)   62.2951% completed.    
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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.    
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succeeded(59)   96.7213% completed.    
succeeded(60)   98.3607% completed.    
succeeded(61)   100% completed.    
1531s 
1531s All commands completed successfully. :-)
1531s 
1531s 
1531s 
1531s ** Harvesting all assembled transcripts into a single multi-fasta file...
1531s 
1531s Monday, November 4, 2024: 14:23:17	CMD: find /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/Trinity.tmp
1531s * [Mon Nov  4 14:23:17 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa 2
1532s * [Mon Nov  4 14:23:18 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta
1533s Monday, November 4, 2024: 14:23:19	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta.gene_trans_map
1533s 
1533s 
1533s #############################################################################
1533s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta
1533s #############################################################################
1533s 
1533s 
1533s ./misc_run_tests/__run_SE_samples_file.sh
1533s 
1533s exit 0
1533s #!/bin/bash -ve
1533s 
1533s ${TRINITY_HOME}/Trinity --samples_file samples.SE.txt \
1533s               --seqType fq \
1533s               --max_memory 1G \
1533s               --output trinity_test_samples_SE
1533s 
1533s 
1533s      ______  ____   ____  ____   ____  ______  __ __
1533s     |      ||    \ |    ||    \ |    ||      ||  |  |
1533s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1533s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1533s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1533s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1533s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1533s 
1533s     Trinity-v2.15.1
1533s 
1533s 
1533s 
1533s Single read files: $VAR1 = [
1533s           'reads.left.fq.gz',
1533s           'reads2.left.fq.gz'
1533s         ];
1533s Monday, November 4, 2024: 14:23:19	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE
1533s Monday, November 4, 2024: 14:23:19	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis
1533s 
1533s 
1533s ----------------------------------------------------------------------------------
1533s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1533s ----------------------------------------------------------------------------------
1533s 
1533s ---------------------------------------------------------------
1533s ------------ In silico Read Normalization ---------------------
1533s -- (Removing Excess Reads Beyond 200 Coverage --
1533s ---------------------------------------------------------------
1533s 
1533s # running normalization on reads: $VAR1 = [
1533s           [
1533s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz',
1533s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz'
1533s           ]
1533s         ];
1533s 
1533s 
1533s Monday, November 4, 2024: 14:23:19	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization --max_CV 10000  --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz
1533s -prepping seqs
1533s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> single.fa
1533s CMD finished (0 seconds)
1533s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz) >> single.fa
1533s CMD finished (0 seconds)
1533s CMD: touch single.fa.ok
1533s CMD finished (0 seconds)
1533s -kmer counting.
1533s -------------------------------------------
1533s ----------- Jellyfish  --------------------
1533s -- (building a k-mer catalog from reads) --
1533s -------------------------------------------
1533s 
1533s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  single.fa
1534s CMD finished (1 seconds)
1534s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1534s CMD finished (0 seconds)
1534s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1534s CMD finished (0 seconds)
1534s CMD: touch jellyfish.K25.min2.kmers.fa.success
1534s CMD finished (0 seconds)
1534s -generating stats files
1534s CMD: /usr/bin/fastaToKmerCoverageStats --reads single.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > single.fa.K25.stats
1534s -reading Kmer occurrences...
1535s 
1535s  done parsing 288470 Kmers, 288470 added, taking 1 seconds.
1535s STATS_GENERATION_TIME: 0 seconds.
1535s CMD finished (1 seconds)
1535s CMD: touch single.fa.K25.stats.ok
1535s CMD finished (0 seconds)
1535s -sorting each stats file by read name.
1535s 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
1535s CMD finished (0 seconds)
1535s CMD: touch single.fa.K25.stats.sort.ok
1535s CMD finished (0 seconds)
1535s -defining normalized reads
1535s 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
1536s 59311 / 61150 = 96.99% reads selected during normalization.
1536s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1536s 0 / 61150 = 0.00% reads discarded as below minimum coverage threshold=1
1536s CMD finished (1 seconds)
1536s CMD: touch single.fa.K25.stats.sort.maxC200.minC1.maxCV10000.accs.ok
1536s CMD finished (0 seconds)
1536s -search and capture.
1536s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz ... done prepping, now search and capture.
1536s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
1536s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz
1537s CMD: touch /tmp/autopkgtest.vWCmNc/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
1537s CMD finished (0 seconds)
1537s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1537s CMD finished (0 seconds)
1537s -removing tmp dir /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/tmp_normalized_reads
1537s 
1537s 
1537s Normalization complete. See outputs: 
1537s 	/tmp/autopkgtest.vWCmNc/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
1537s Monday, November 4, 2024: 14:23:23	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/normalization.ok
1537s Monday, November 4, 2024: 14:23:23	CMD: cat /tmp/autopkgtest.vWCmNc/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
1537s Monday, November 4, 2024: 14:23:23	CMD: touch single.fa.ok
1537s Monday, November 4, 2024: 14:23:23	CMD: touch single.fa.ok
1537s -------------------------------------------
1537s ----------- Jellyfish  --------------------
1537s -- (building a k-mer (25) catalog from reads) --
1537s -------------------------------------------
1537s 
1537s * [Mon Nov  4 14:23:23 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa
1538s * [Mon Nov  4 14:23:24 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
1538s * [Mon Nov  4 14:23:24 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
1538s ----------------------------------------------
1538s --------------- Inchworm (K=25, asm) ---------------------
1538s -- (Linear contig construction from k-mers) --
1538s ----------------------------------------------
1538s 
1538s * [Mon Nov  4 14:23:24 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa.tmp
1538s Kmer length set to: 25
1538s Min assembly length set to: 25
1538s Monitor turned on, set to: 1
1538s double stranded mode set
1538s min entropy set to: 1
1538s setting number of threads to: 2
1538s -setting parallel iworm mode.
1538s -reading Kmer occurrences...
1538s 
 [0M] Kmers parsed.     
1538s  done parsing 287930 Kmers, 287930 added, taking 0 seconds.
1538s 
1538s TIMING KMER_DB_BUILDING 0 s.
1538s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
1538s Pruned 2078 kmers from catalog.
1538s 	Pruning time: 0 seconds = 0 minutes.
1538s 
1538s TIMING PRUNING 0 s.
1538s -populating the kmer seed candidate list.
1538s Kcounter hash size: 287930
1538s Processed 285852 non-zero abundance kmers in kcounter.
1538s -Not sorting list of kmers, given parallel mode in effect.
1538s -beginning inchworm contig assembly.
1538s Total kcounter hash size: 287930 vs. sorted list size: 285852
1538s num threads set to: 2
1538s Done opening file. tmp.iworm.fa.pid_70846.thread_0
1538s Done opening file. tmp.iworm.fa.pid_70846.thread_1
1539s 
1539s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
1539s 
1539s TIMING CONTIG_BUILDING 1 s.
1539s 
1539s TIMING PROG_RUNTIME 1 s.
1539s * [Mon Nov  4 14:23:25 2024] Running CMD: mv /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa.tmp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa
1539s Monday, November 4, 2024: 14:23:25	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa.finished
1539s --------------------------------------------------------
1539s -------------------- Chrysalis -------------------------
1539s -- (Contig Clustering & de Bruijn Graph Construction) --
1539s --------------------------------------------------------
1539s 
1539s inchworm_target: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa
1539s bowtie_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa
1539s chrysalis_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa
1539s * [Mon Nov  4 14:23:25 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa 100 10 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100
1539s * [Mon Nov  4 14:23:25 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt
1541s * [Mon Nov  4 14:23:27 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G  -k9,9gr /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted
1541s * [Mon Nov  4 14:23:27 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1541s * [Mon Nov  4 14:23:27 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100  -weld_graph /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/GraphFromIwormFasta.out
1541s * [Mon Nov  4 14:23:27 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/bundled_iworm_contigs.fasta -min 200
1541s * [Mon Nov  4 14:23:27 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa -f /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -p 10 
1544s * [Mon Nov  4 14:23:30 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/readsToComponents.out > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/readsToComponents.out.sort
1544s Monday, November 4, 2024: 14:23:30	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/read_partitions/Fb_0/CBin_0
1544s Monday, November 4, 2024: 14:23:30	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/partitioned_reads.files.list.ok
1544s Monday, November 4, 2024: 14:23:30	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.vWCmNc/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
1544s Monday, November 4, 2024: 14:23:30	CMD: touch recursive_trinity.cmds.ok
1544s Monday, November 4, 2024: 14:23:30	CMD: touch recursive_trinity.cmds.ok
1544s 
1544s 
1544s --------------------------------------------------------------------------------
1544s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1544s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1544s --------------------------------------------------------------------------------
1544s 
1544s Monday, November 4, 2024: 14:23:30	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
1544s Number of Commands: 45
1607s 
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.    
1607s 
1607s All commands completed successfully. :-)
1607s 
1607s 
1607s 
1607s ** Harvesting all assembled transcripts into a single multi-fasta file...
1607s 
1607s Monday, November 4, 2024: 14:24:33	CMD: find /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/Trinity.tmp
1607s * [Mon Nov  4 14:24:33 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa 2
1609s * [Mon Nov  4 14:24:35 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta
1609s Monday, November 4, 2024: 14:24:35	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta.gene_trans_map
1609s 
1609s 
1609s #############################################################################
1609s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta
1609s #############################################################################
1609s 
1609s 
1609s 
1609s 
1609s exit 0
1609s #!/bin/bash -ve
1609s 
1609s 
1609s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
1609s     gunzip -c reads.right.fq.gz > reads.right.fq
1609s fi
1609s 
1609s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
1609s     gunzip -c reads.left.fq.gz > reads.left.fq
1609s fi
1609s 
1609s 
1609s 
1609s #######################################################
1609s ##  Run Trinity to Generate Transcriptome Assemblies ##
1609s #######################################################
1609s 
1609s CPU=$(nproc || sysctl -n hw.physicalcpu)
1609s 
1609s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \
1609s               --left reads.left.fq \
1609s               --right reads.right.fq \
1609s               --SS_lib_type RF \
1609s               --CPU ${CPU}\
1609s               --output trinity_with_workdir \
1609s               --workdir  /tmp/trinity.workdir.$$ --full_cleanup
1609s ./misc_run_tests/__runMe_use_workdir.sh
1609s 
1609s 
1609s      ______  ____   ____  ____   ____  ______  __ __
1609s     |      ||    \ |    ||    \ |    ||      ||  |  |
1609s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1609s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1609s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1609s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1609s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1609s 
1609s     Trinity-v2.15.1
1609s 
1609s 
1609s 
1609s Left read files: $VAR1 = [
1609s           'reads.left.fq'
1609s         ];
1609s Right read files: $VAR1 = [
1609s           'reads.right.fq'
1609s         ];
1609s Monday, November 4, 2024: 14:24:35	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir
1609s Monday, November 4, 2024: 14:24:35	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis
1609s 
1609s 
1609s ----------------------------------------------------------------------------------
1609s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1609s ----------------------------------------------------------------------------------
1609s 
1609s ---------------------------------------------------------------
1609s ------------ In silico Read Normalization ---------------------
1609s -- (Removing Excess Reads Beyond 200 Coverage --
1609s ---------------------------------------------------------------
1609s 
1609s # running normalization on reads: $VAR1 = [
1609s           [
1609s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq'
1609s           ],
1609s           [
1609s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq'
1609s           ]
1609s         ];
1609s 
1609s 
1609s Monday, November 4, 2024: 14:24:35	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization --max_CV 10000  --SS_lib_type RF  --left /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq --right /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq --pairs_together  --PARALLEL_STATS  
1609s -prepping seqs
1609s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq >> left.fa
1609s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq >> right.fa
1609s CMD finished (0 seconds)
1609s CMD finished (0 seconds)
1609s CMD: touch left.fa.ok
1609s CMD finished (0 seconds)
1609s CMD: touch right.fa.ok
1609s CMD finished (0 seconds)
1609s Done converting input files.CMD: cat left.fa right.fa > both.fa
1609s CMD finished (0 seconds)
1609s CMD: touch both.fa.ok
1609s CMD finished (0 seconds)
1609s -kmer counting.
1609s -------------------------------------------
1609s ----------- Jellyfish  --------------------
1609s -- (building a k-mer catalog from reads) --
1609s -------------------------------------------
1609s 
1609s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
1610s CMD finished (1 seconds)
1610s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1610s CMD finished (0 seconds)
1610s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1610s CMD finished (0 seconds)
1610s CMD: touch jellyfish.K25.min2.kmers.fa.success
1610s CMD finished (0 seconds)
1610s -generating stats files
1610s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
1610s -reading Kmer occurrences...
1610s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
1610s -reading Kmer occurrences...
1610s 
1610s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
1610s 
1610s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
1611s STATS_GENERATION_TIME: 1 seconds.
1611s CMD finished (1 seconds)
1611s STATS_GENERATION_TIME: 1 seconds.
1611s CMD finished (1 seconds)
1611s CMD: touch left.fa.K25.stats.ok
1611s CMD finished (0 seconds)
1611s CMD: touch right.fa.K25.stats.ok
1611s CMD finished (0 seconds)
1611s -sorting each stats file by read name.
1611s 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
1611s 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
1611s CMD finished (0 seconds)
1611s CMD finished (0 seconds)
1611s CMD: touch left.fa.K25.stats.sort.ok
1611s CMD finished (0 seconds)
1611s CMD: touch right.fa.K25.stats.sort.ok
1611s CMD finished (0 seconds)
1611s -defining normalized reads
1611s 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
1611s -opening left.fa.K25.stats.sort
1611s -opening right.fa.K25.stats.sort
1611s -done opening files.
1611s CMD finished (0 seconds)
1611s CMD: touch pairs.K25.stats.ok
1611s CMD finished (0 seconds)
1611s 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
1612s 30472 / 30575 = 99.66% reads selected during normalization.
1612s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1612s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
1612s CMD finished (1 seconds)
1612s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
1612s CMD finished (0 seconds)
1612s -search and capture.
1612s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq ... done prepping, now search and capture.
1612s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq
1612s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq ... done prepping, now search and capture.
1612s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq
1612s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.left.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
1612s CMD finished (0 seconds)
1612s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.right.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
1612s CMD finished (0 seconds)
1612s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1612s CMD finished (0 seconds)
1612s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1612s CMD finished (0 seconds)
1612s -removing tmp dir /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/tmp_normalized_reads
1612s 
1612s 
1612s Normalization complete. See outputs: 
1612s 	/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.left.fq.normalized_K25_maxC200_minC1_maxCV10000.fq
1612s 	/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.right.fq.normalized_K25_maxC200_minC1_maxCV10000.fq
1612s Monday, November 4, 2024: 14:24:38	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/normalization.ok
1612s Converting input files. (in parallel)Monday, November 4, 2024: 14:24:38	CMD: cat /tmp/autopkgtest.vWCmNc/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
1612s Monday, November 4, 2024: 14:24:38	CMD: cat /tmp/autopkgtest.vWCmNc/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
1612s Monday, November 4, 2024: 14:24:38	CMD: touch right.fa.ok
1612s Monday, November 4, 2024: 14:24:38	CMD: touch left.fa.ok
1612s Monday, November 4, 2024: 14:24:38	CMD: touch left.fa.ok right.fa.ok
1612s Monday, November 4, 2024: 14:24:38	CMD: cat left.fa right.fa > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
1612s Monday, November 4, 2024: 14:24:38	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa.ok
1612s -------------------------------------------
1612s ----------- Jellyfish  --------------------
1612s -- (building a k-mer (25) catalog from reads) --
1612s -------------------------------------------
1612s 
1612s * [Mon Nov  4 14:24:38 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
1614s * [Mon Nov  4 14:24:40 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
1614s * [Mon Nov  4 14:24:40 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
1614s ----------------------------------------------
1614s --------------- Inchworm (K=25, asm) ---------------------
1614s -- (Linear contig construction from k-mers) --
1614s ----------------------------------------------
1614s 
1614s * [Mon Nov  4 14:24:40 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa.tmp
1614s Kmer length set to: 25
1614s Min assembly length set to: 25
1614s Monitor turned on, set to: 1
1614s min entropy set to: 1
1614s setting number of threads to: 2
1614s -setting parallel iworm mode.
1614s -reading Kmer occurrences...
1614s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
1614s  done parsing 519541 Kmers, 519541 added, taking 0 seconds.
1614s 
1614s TIMING KMER_DB_BUILDING 0 s.
1614s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
1614s Pruned 4252 kmers from catalog.
1614s 	Pruning time: 0 seconds = 0 minutes.
1614s 
1614s TIMING PRUNING 0 s.
1614s -populating the kmer seed candidate list.
1614s Kcounter hash size: 519541
1614s Processed 515289 non-zero abundance kmers in kcounter.
1614s -Not sorting list of kmers, given parallel mode in effect.
1614s -beginning inchworm contig assembly.
1614s Total kcounter hash size: 519541 vs. sorted list size: 515289
1614s num threads set to: 2
1614s Done opening file. tmp.iworm.fa.pid_77747.thread_0
1614s Done opening file. tmp.iworm.fa.pid_77747.thread_1
1615s 
1615s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
1615s 
1615s TIMING CONTIG_BUILDING 1 s.
1615s 
1615s TIMING PROG_RUNTIME 1 s.
1615s * [Mon Nov  4 14:24:41 2024] Running CMD: mv /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa.tmp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa
1615s Monday, November 4, 2024: 14:24:41	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa.finished
1615s --------------------------------------------------------
1615s -------------------- Chrysalis -------------------------
1615s -- (Contig Clustering & de Bruijn Graph Construction) --
1615s --------------------------------------------------------
1615s 
1615s inchworm_target: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
1615s bowtie_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
1615s chrysalis_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
1615s * [Mon Nov  4 14:24:41 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa 100 10 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100
1615s * [Mon Nov  4 14:24:41 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 1>/dev/null
1615s * [Mon Nov  4 14:24:41 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm.bowtie.nameSorted.bam" 
1619s * [Mon Nov  4 14:24:45 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_scaffolds.txt
1619s * [Mon Nov  4 14:24:45 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt
1620s * [Mon Nov  4 14:24:46 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted
1620s * [Mon Nov  4 14:24:46 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1620s * [Mon Nov  4 14:24:46 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/GraphFromIwormFasta.out
1620s * [Mon Nov  4 14:24:46 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/bundled_iworm_contigs.fasta -min 200
1620s * [Mon Nov  4 14:24:46 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa -f /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -strand  -p 10 
1622s * [Mon Nov  4 14:24:48 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/readsToComponents.out > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/readsToComponents.out.sort
1622s Monday, November 4, 2024: 14:24:48	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/read_partitions/Fb_0/CBin_0
1622s Monday, November 4, 2024: 14:24:48	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/partitioned_reads.files.list.ok
1622s Monday, November 4, 2024: 14:24:48	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.vWCmNc/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.77608  --no_salmon  > recursive_trinity.cmds
1622s Monday, November 4, 2024: 14:24:48	CMD: touch recursive_trinity.cmds.ok
1622s Monday, November 4, 2024: 14:24:48	CMD: touch recursive_trinity.cmds.ok
1622s 
1622s 
1622s --------------------------------------------------------------------------------
1622s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1622s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1622s --------------------------------------------------------------------------------
1622s 
1622s Monday, November 4, 2024: 14:24:48	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
1622s Number of Commands: 39
1684s 
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.    
1684s 
1684s All commands completed successfully. :-)
1684s 
1684s 
1684s 
1684s ** Harvesting all assembled transcripts into a single multi-fasta file...
1684s 
1684s Monday, November 4, 2024: 14:25:50	CMD: find /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/Trinity.tmp
1684s * [Mon Nov  4 14:25:50 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa 2
1685s * [Mon Nov  4 14:25:51 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta
1685s 
1685s 
1685s #############################################################################
1685s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta
1685s #############################################################################
1685s 
1685s 
1685s Monday, November 4, 2024: 14:25:51	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta.gene_trans_map
1685s ./misc_run_tests/__runMe_piecemeal.sh
1685s 
1685s 
1685s exit 0
1685s #!/bin/bash -ve
1685s 
1685s #######################################################
1685s ##  Run Trinity to Generate Transcriptome Assemblies ##
1685s #######################################################
1685s 
1685s CPU=$(nproc || sysctl -n hw.physicalcpu)
1685s 
1685s # stop before inchworm (just in silico norm)
1685s ${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
1685s 
1685s 
1685s      ______  ____   ____  ____   ____  ______  __ __
1685s     |      ||    \ |    ||    \ |    ||      ||  |  |
1685s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1685s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1685s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1685s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1685s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1685s 
1685s     Trinity-v2.15.1
1685s 
1685s 
1685s 
1685s Left read files: $VAR1 = [
1685s           'reads.left.fq.gz'
1685s         ];
1685s Right read files: $VAR1 = [
1685s           'reads.right.fq.gz'
1685s         ];
1685s Monday, November 4, 2024: 14:25:51	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal
1685s Monday, November 4, 2024: 14:25:51	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis
1685s 
1685s 
1685s ----------------------------------------------------------------------------------
1685s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1685s ----------------------------------------------------------------------------------
1685s 
1685s ---------------------------------------------------------------
1685s ------------ In silico Read Normalization ---------------------
1685s -- (Removing Excess Reads Beyond 200 Coverage --
1685s ---------------------------------------------------------------
1685s 
1685s # running normalization on reads: $VAR1 = [
1685s           [
1685s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
1685s           ],
1685s           [
1685s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
1685s           ]
1685s         ];
1685s 
1685s 
1685s Monday, November 4, 2024: 14:25:51	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization --max_CV 10000  --left /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together  --PARALLEL_STATS  
1685s -prepping seqs
1685s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
1685s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
1685s CMD finished (0 seconds)
1685s CMD finished (0 seconds)
1685s CMD: touch left.fa.ok
1685s CMD finished (0 seconds)
1685s CMD: touch right.fa.ok
1685s CMD finished (0 seconds)
1685s Done converting input files.CMD: cat left.fa right.fa > both.fa
1685s CMD finished (0 seconds)
1685s CMD: touch both.fa.ok
1685s CMD finished (0 seconds)
1685s -kmer counting.
1685s -------------------------------------------
1685s ----------- Jellyfish  --------------------
1685s -- (building a k-mer catalog from reads) --
1685s -------------------------------------------
1685s 
1685s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  both.fa
1687s CMD finished (2 seconds)
1687s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1687s CMD finished (0 seconds)
1687s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1687s CMD finished (0 seconds)
1687s CMD: touch jellyfish.K25.min2.kmers.fa.success
1687s CMD finished (0 seconds)
1687s -generating stats files
1687s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > left.fa.K25.stats
1687s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > right.fa.K25.stats
1687s -reading Kmer occurrences...
1687s -reading Kmer occurrences...
1687s 
1687s  done parsing 100964 Kmers, 100964 added, taking 0 seconds.
1687s 
1687s  done parsing 100964 Kmers, 100964 added, taking 0 seconds.
1687s STATS_GENERATION_TIME: 0 seconds.
1687s CMD finished (0 seconds)
1687s STATS_GENERATION_TIME: 0 seconds.
1687s CMD finished (0 seconds)
1687s CMD: touch left.fa.K25.stats.ok
1687s CMD finished (0 seconds)
1687s CMD: touch right.fa.K25.stats.ok
1687s CMD finished (0 seconds)
1688s -sorting each stats file by read name.
1688s 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
1688s 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
1688s CMD finished (0 seconds)
1688s CMD finished (0 seconds)
1688s CMD: touch left.fa.K25.stats.sort.ok
1688s CMD finished (0 seconds)
1688s CMD: touch right.fa.K25.stats.sort.ok
1688s CMD finished (0 seconds)
1688s -defining normalized reads
1688s 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
1688s -opening left.fa.K25.stats.sort
1688s -opening right.fa.K25.stats.sort
1688s -done opening files.
1688s CMD finished (0 seconds)
1688s CMD: touch pairs.K25.stats.ok
1688s CMD finished (0 seconds)
1688s 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
1688s 30472 / 30575 = 99.66% reads selected during normalization.
1688s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1688s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
1688s CMD finished (0 seconds)
1688s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
1688s CMD finished (0 seconds)
1688s -search and capture.
1688s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture.
1688s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
1688s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture.
1688s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
1689s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
1689s CMD finished (0 seconds)
1689s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
1689s CMD finished (0 seconds)
1689s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1689s CMD finished (0 seconds)
1689s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1689s CMD finished (0 seconds)
1689s -removing tmp dir /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/tmp_normalized_reads
1689s 
1689s 
1689s Normalization complete. See outputs: 
1689s 	/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
1689s 	/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
1689s Monday, November 4, 2024: 14:25:55	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/normalization.ok
1689s Converting input files. (in parallel)Monday, November 4, 2024: 14:25:55	CMD: cat /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -A -R 1 - >> left.fa
1689s Monday, November 4, 2024: 14:25:55	CMD: cat /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa
1689s Monday, November 4, 2024: 14:25:55	CMD: touch left.fa.ok
1689s Monday, November 4, 2024: 14:25:55	CMD: touch right.fa.ok
1689s Monday, November 4, 2024: 14:25:55	CMD: touch left.fa.ok right.fa.ok
1689s Monday, November 4, 2024: 14:25:55	CMD: cat left.fa right.fa > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1689s Monday, November 4, 2024: 14:25:55	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa.ok
1689s WARNING:  --no_run_inchworm parameter in effect.  Stopping here prior to running inchworm.
1689s 
1689s # stop before chrysalis
1689s ${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
1689s 
1689s 
1689s      ______  ____   ____  ____   ____  ______  __ __
1689s     |      ||    \ |    ||    \ |    ||      ||  |  |
1689s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1689s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1689s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1689s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1689s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1689s 
1689s     Trinity-v2.15.1
1689s 
1689s 
1689s 
1689s Left read files: $VAR1 = [
1689s           'reads.left.fq.gz'
1689s         ];
1689s Right read files: $VAR1 = [
1689s           'reads.right.fq.gz'
1689s         ];
1689s 
1689s 
1689s ----------------------------------------------------------------------------------
1689s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1689s ----------------------------------------------------------------------------------
1689s 
1689s ---------------------------------------------------------------
1689s ------------ In silico Read Normalization ---------------------
1689s -- (Removing Excess Reads Beyond 200 Coverage --
1689s ---------------------------------------------------------------
1689s 
1689s # running normalization on reads: $VAR1 = [
1689s           [
1689s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
1689s           ],
1689s           [
1689s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
1689s           ]
1689s         ];
1689s 
1689s 
1689s -------------------------------------------
1689s ----------- Jellyfish  --------------------
1689s -- (building a k-mer (25) catalog from reads) --
1689s -------------------------------------------
1689s 
1689s * [Mon Nov  4 14:25:55 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1690s * [Mon Nov  4 14:25:56 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
1691s * [Mon Nov  4 14:25:57 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
1691s ----------------------------------------------
1691s --------------- Inchworm (K=25, asm) ---------------------
1691s -- (Linear contig construction from k-mers) --
1691s ----------------------------------------------
1691s 
1691s * [Mon Nov  4 14:25:57 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa.tmp
1691s Kmer length set to: 25
1691s Min assembly length set to: 25
1691s Monitor turned on, set to: 1
1691s double stranded mode set
1691s min entropy set to: 1
1691s setting number of threads to: 2
1691s -setting parallel iworm mode.
1691s -reading Kmer occurrences...
1691s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
1691s  done parsing 517949 Kmers, 517949 added, taking 0 seconds.
1691s 
1691s TIMING KMER_DB_BUILDING 0 s.
1691s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
1691s Pruned 4114 kmers from catalog.
1691s 	Pruning time: 0 seconds = 0 minutes.
1691s 
1691s TIMING PRUNING 0 s.
1691s -populating the kmer seed candidate list.
1691s Kcounter hash size: 517949
1691s Processed 513835 non-zero abundance kmers in kcounter.
1691s -Not sorting list of kmers, given parallel mode in effect.
1691s -beginning inchworm contig assembly.
1691s Total kcounter hash size: 517949 vs. sorted list size: 513835
1691s num threads set to: 2
1691s Done opening file. tmp.iworm.fa.pid_84864.thread_0
1691s Done opening file. tmp.iworm.fa.pid_84864.thread_1
1692s 
1692s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
1692s 
1692s TIMING CONTIG_BUILDING 1 s.
1692s 
1692s TIMING PROG_RUNTIME 1 s.
1692s * [Mon Nov  4 14:25:58 2024] Running CMD: mv /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa.tmp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa
1692s Monday, November 4, 2024: 14:25:58	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa.finished
1692s 
1692s 
1692s 
1692s #########################################################################
1692s Inchworm is complete.  --no_run_chrysalis was specified, so stopping here.
1692s #########################################################################
1692s 
1692s 
1692s 
1692s # stop before phase 2
1692s ${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
1692s 
1692s 
1692s      ______  ____   ____  ____   ____  ______  __ __
1692s     |      ||    \ |    ||    \ |    ||      ||  |  |
1692s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1692s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1692s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1692s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1692s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1692s 
1692s     Trinity-v2.15.1
1692s 
1692s 
1692s 
1692s Left read files: $VAR1 = [
1692s           'reads.left.fq.gz'
1692s         ];
1692s Right read files: $VAR1 = [
1692s           'reads.right.fq.gz'
1692s         ];
1692s 
1692s 
1692s ----------------------------------------------------------------------------------
1692s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1692s ----------------------------------------------------------------------------------
1692s 
1692s ---------------------------------------------------------------
1692s ------------ In silico Read Normalization ---------------------
1692s -- (Removing Excess Reads Beyond 200 Coverage --
1692s ---------------------------------------------------------------
1692s 
1692s # running normalization on reads: $VAR1 = [
1692s           [
1692s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
1692s           ],
1692s           [
1692s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
1692s           ]
1692s         ];
1692s 
1692s 
1692s --------------------------------------------------------
1692s -------------------- Chrysalis -------------------------
1692s -- (Contig Clustering & de Bruijn Graph Construction) --
1692s --------------------------------------------------------
1692s 
1692s inchworm_target: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1692s bowtie_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1692s chrysalis_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1692s 
1692s 
1692s #######################################################################
1692s Inchworm file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa detected.
1692s Skipping Inchworm Step, Using Previous Inchworm Assembly
1692s #######################################################################
1692s 
1692s * [Mon Nov  4 14:25:58 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa 100 10 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100
1692s * [Mon Nov  4 14:25:58 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 1>/dev/null
1693s * [Mon Nov  4 14:25:59 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam" 
1696s * [Mon Nov  4 14:26:02 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt
1697s * [Mon Nov  4 14:26:02 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt
1698s * [Mon Nov  4 14:26:04 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted
1698s * [Mon Nov  4 14:26:04 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1698s * [Mon Nov  4 14:26:04 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100  -weld_graph /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out
1698s * [Mon Nov  4 14:26:04 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -min 200
1698s * [Mon Nov  4 14:26:04 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa -f /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -p 10 
1701s * [Mon Nov  4 14:26:07 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.sort
1701s Monday, November 4, 2024: 14:26:07	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/read_partitions/Fb_0/CBin_0
1701s Monday, November 4, 2024: 14:26:07	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/partitioned_reads.files.list.ok
1701s Monday, November 4, 2024: 14:26:07	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.vWCmNc/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
1701s Monday, November 4, 2024: 14:26:07	CMD: touch recursive_trinity.cmds.ok
1701s Monday, November 4, 2024: 14:26:07	CMD: touch recursive_trinity.cmds.ok
1701s 
1701s # finish it up
1701s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz  --CPU ${CPU} --output trinity_piecemeal 
1701s 
1701s 
1701s ###################################################################
1701s ##  Stopping here due to --no_distributed_trinity_exec in effect ##
1701s ###################################################################
1701s 
1701s 
1701s 
1701s      ______  ____   ____  ____   ____  ______  __ __
1701s     |      ||    \ |    ||    \ |    ||      ||  |  |
1701s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1701s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1701s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1701s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1701s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1701s 
1701s     Trinity-v2.15.1
1701s 
1701s 
1701s 
1701s Left read files: $VAR1 = [
1701s           'reads.left.fq.gz'
1701s         ];
1701s Right read files: $VAR1 = [
1701s           'reads.right.fq.gz'
1701s         ];
1701s 
1701s 
1701s ----------------------------------------------------------------------------------
1701s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1701s ----------------------------------------------------------------------------------
1701s 
1701s ---------------------------------------------------------------
1701s ------------ In silico Read Normalization ---------------------
1701s -- (Removing Excess Reads Beyond 200 Coverage --
1701s ---------------------------------------------------------------
1701s 
1701s # running normalization on reads: $VAR1 = [
1701s           [
1701s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
1701s           ],
1701s           [
1701s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
1701s           ]
1701s         ];
1701s 
1701s 
1701s --------------------------------------------------------
1701s -------------------- Chrysalis -------------------------
1701s -- (Contig Clustering & de Bruijn Graph Construction) --
1701s --------------------------------------------------------
1701s 
1701s inchworm_target: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1701s bowtie_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1701s chrysalis_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1701s 
1701s 
1701s #######################################################################
1701s Inchworm file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa detected.
1701s Skipping Inchworm Step, Using Previous Inchworm Assembly
1701s #######################################################################
1701s 
1701s -- Skipping CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa 100 10 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100, checkpoint [/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100.ok] exists.
1701s -- Skipping CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 1>/dev/null, checkpoint [/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100.bowtie2-build.ok] exists.
1701s -- 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam" , checkpoint [/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam.ok] exists.
1701s -- Skipping CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt, checkpoint [/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt.ok] exists.
1701s -- Skipping CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt, checkpoint [/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.ok] exists.
1701s -- Skipping CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted, checkpoint [/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.ok] exists.
1701s -- Skipping CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames, checkpoint [/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames.ok] exists.
1701s -- Skipping CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100  -weld_graph /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out, checkpoint [/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out.ok] exists.
1701s -- Skipping CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -min 200, checkpoint [/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta.ok] exists.
1701s -- Skipping CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa -f /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -p 10 , checkpoint [/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.ok] exists.
1701s -- Skipping CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.sort, checkpoint [/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.sort.ok] exists.
1701s 
1701s 
1701s --------------------------------------------------------------------------------
1701s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1701s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1701s --------------------------------------------------------------------------------
1701s 
1701s Monday, November 4, 2024: 14:26:07	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
1701s Number of Commands: 38
1762s 
succeeded(1)   2.63158% completed.    
succeeded(2)   5.26316% completed.    
succeeded(3)   7.89474% completed.    
succeeded(4)   10.5263% completed.    
succeeded(5)   13.1579% completed.    
succeeded(6)   15.7895% completed.    
succeeded(7)   18.4211% completed.    
succeeded(8)   21.0526% completed.    
succeeded(9)   23.6842% completed.    
succeeded(10)   26.3158% completed.    
succeeded(11)   28.9474% completed.    
succeeded(12)   31.5789% completed.    
succeeded(13)   34.2105% completed.    
succeeded(14)   36.8421% completed.    
succeeded(15)   39.4737% completed.    
succeeded(16)   42.1053% completed.    
succeeded(17)   44.7368% completed.    
succeeded(18)   47.3684% completed.    
succeeded(19)   50% completed.    
succeeded(20)   52.6316% completed.    
succeeded(21)   55.2632% completed.    
succeeded(22)   57.8947% completed.    
succeeded(23)   60.5263% completed.    
succeeded(24)   63.1579% completed.    
succeeded(25)   65.7895% completed.    
succeeded(26)   68.4211% completed.    
succeeded(27)   71.0526% completed.    
succeeded(28)   73.6842% completed.    
succeeded(29)   76.3158% completed.    
succeeded(30)   78.9474% completed.    
succeeded(31)   81.5789% completed.    
succeeded(32)   84.2105% completed.    
succeeded(33)   86.8421% completed.    
succeeded(34)   89.4737% completed.    
succeeded(35)   92.1053% completed.    
succeeded(36)   94.7368% completed.    
succeeded(37)   97.3684% completed.    
succeeded(38)   100% completed.    
1762s 
1762s All commands completed successfully. :-)
1762s 
1762s 
1762s 
1762s ** Harvesting all assembled transcripts into a single multi-fasta file...
1762s 
1762s Monday, November 4, 2024: 14:27:08	CMD: find /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/Trinity.tmp
1762s * [Mon Nov  4 14:27:08 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 2
1763s * [Mon Nov  4 14:27:09 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta
1763s Monday, November 4, 2024: 14:27:09	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta.gene_trans_map
1763s 
1763s 
1763s #############################################################################
1763s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta
1763s #############################################################################
1763s 
1763s 
1763s 
1763s 
1763s 
1763s 
1763s ##### Done Running Trinity #####
1763s 
1763s exit 0
1763s ./misc_run_tests/__run_PE_samples_file.min_kmer_cov_3.sh
1763s #!/bin/bash -ve
1763s 
1763s ${TRINITY_HOME}/Trinity --samples_file samples.PE.txt \
1763s               --seqType fq \
1763s               --max_memory 1G \
1763s               --min_kmer_cov 3 \
1763s               --output trinity_test_samples_PE_min_kmer_cov_3
1763s 
1763s 
1763s      ______  ____   ____  ____   ____  ______  __ __
1763s     |      ||    \ |    ||    \ |    ||      ||  |  |
1763s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1763s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1763s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1763s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1763s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1763s 
1763s     Trinity-v2.15.1
1763s 
1763s 
1763s 
1763s Left read files: $VAR1 = [
1763s           'reads.left.fq.gz',
1763s           'reads2.left.fq.gz'
1763s         ];
1763s Right read files: $VAR1 = [
1763s           'reads.right.fq.gz',
1763s           'reads2.right.fq.gz'
1763s         ];
1763s Monday, November 4, 2024: 14:27:09	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3
1763s Monday, November 4, 2024: 14:27:09	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis
1763s 
1763s 
1763s ----------------------------------------------------------------------------------
1763s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1763s ----------------------------------------------------------------------------------
1763s 
1763s ---------------------------------------------------------------
1763s ------------ In silico Read Normalization ---------------------
1763s -- (Removing Excess Reads Beyond 200 Coverage --
1763s ---------------------------------------------------------------
1763s 
1763s # running normalization on reads: $VAR1 = [
1763s           [
1763s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz',
1763s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz'
1763s           ],
1763s           [
1763s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz',
1763s             '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz'
1763s           ]
1763s         ];
1763s 
1763s 
1763s Monday, November 4, 2024: 14:27:09	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G  --max_cov 200 --min_cov 3 --CPU 2 --output /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz --right /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz,/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz --pairs_together  --PARALLEL_STATS  
1763s -prepping seqs
1764s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
1764s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
1764s CMD finished (0 seconds)
1764s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz) >> left.fa
1764s CMD finished (0 seconds)
1764s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz) >> right.fa
1764s CMD finished (0 seconds)
1764s CMD finished (0 seconds)
1764s CMD: touch left.fa.ok
1764s CMD finished (0 seconds)
1764s CMD: touch right.fa.ok
1764s CMD finished (0 seconds)
1764s Done converting input files.CMD: cat left.fa right.fa > both.fa
1764s CMD finished (0 seconds)
1764s CMD: touch both.fa.ok
1764s CMD finished (0 seconds)
1764s -kmer counting.
1764s -------------------------------------------
1764s ----------- Jellyfish  --------------------
1764s -- (building a k-mer catalog from reads) --
1764s -------------------------------------------
1764s 
1764s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  both.fa
1765s CMD finished (1 seconds)
1765s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1765s CMD finished (0 seconds)
1765s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1765s CMD finished (0 seconds)
1765s CMD: touch jellyfish.K25.min2.kmers.fa.success
1765s CMD finished (0 seconds)
1765s -generating stats files
1765s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > left.fa.K25.stats
1765s -reading Kmer occurrences...
1765s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > right.fa.K25.stats
1765s -reading Kmer occurrences...
1766s 
1766s  done parsing 518514 Kmers, 518514 added, taking 1 seconds.
1766s 
1766s  done parsing 518514 Kmers, 518514 added, taking 1 seconds.
1767s STATS_GENERATION_TIME: 1 seconds.
1767s STATS_GENERATION_TIME: 1 seconds.
1767s CMD finished (2 seconds)
1767s CMD finished (2 seconds)
1767s CMD: touch left.fa.K25.stats.ok
1767s CMD finished (0 seconds)
1767s CMD: touch right.fa.K25.stats.ok
1767s CMD finished (0 seconds)
1767s -sorting each stats file by read name.
1767s 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
1767s 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
1767s CMD finished (0 seconds)
1767s CMD finished (0 seconds)
1767s CMD: touch left.fa.K25.stats.sort.ok
1767s CMD finished (0 seconds)
1767s CMD: touch right.fa.K25.stats.sort.ok
1767s CMD finished (0 seconds)
1767s -defining normalized reads
1767s 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
1767s -opening left.fa.K25.stats.sort
1767s -opening right.fa.K25.stats.sort
1767s -done opening files.
1768s CMD finished (1 seconds)
1768s CMD: touch pairs.K25.stats.ok
1768s CMD finished (0 seconds)
1768s 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
1768s 53574 / 61150 = 87.61% reads selected during normalization.
1768s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1768s 2974 / 61150 = 4.86% reads discarded as below minimum coverage threshold=3
1768s CMD finished (0 seconds)
1768s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
1768s CMD finished (0 seconds)
1768s -search and capture.
1769s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz ... done prepping, now search and capture.
1769s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
1769s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz ... done prepping, now search and capture.
1769s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
1769s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz
1769s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz
1769s CMD: touch /tmp/autopkgtest.vWCmNc/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
1769s CMD finished (0 seconds)
1769s CMD: touch /tmp/autopkgtest.vWCmNc/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
1769s CMD finished (0 seconds)
1769s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1770s CMD finished (0 seconds)
1770s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
1770s CMD finished (0 seconds)
1770s -removing tmp dir /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/tmp_normalized_reads
1770s 
1770s 
1770s Normalization complete. See outputs: 
1770s 	/tmp/autopkgtest.vWCmNc/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
1770s 	/tmp/autopkgtest.vWCmNc/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
1770s Monday, November 4, 2024: 14:27:16	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/normalization.ok
1770s Converting input files. (in parallel)Monday, November 4, 2024: 14:27:16	CMD: cat /tmp/autopkgtest.vWCmNc/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
1770s Monday, November 4, 2024: 14:27:16	CMD: cat /tmp/autopkgtest.vWCmNc/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
1770s Monday, November 4, 2024: 14:27:16	CMD: touch right.fa.ok
1770s Monday, November 4, 2024: 14:27:16	CMD: touch left.fa.ok
1770s Monday, November 4, 2024: 14:27:16	CMD: touch left.fa.ok right.fa.ok
1770s Monday, November 4, 2024: 14:27:16	CMD: cat left.fa right.fa > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
1770s Monday, November 4, 2024: 14:27:16	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa.ok
1770s -------------------------------------------
1770s ----------- Jellyfish  --------------------
1770s -- (building a k-mer (25) catalog from reads) --
1770s -------------------------------------------
1770s 
1770s * [Mon Nov  4 14:27:16 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
1771s * [Mon Nov  4 14:27:17 2024] Running CMD: jellyfish dump -L 3 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
1771s * [Mon Nov  4 14:27:17 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
1771s ----------------------------------------------
1771s --------------- Inchworm (K=25, asm) ---------------------
1771s -- (Linear contig construction from k-mers) --
1771s ----------------------------------------------
1771s 
1771s * [Mon Nov  4 14:27:17 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa.tmp
1771s Kmer length set to: 25
1771s Min assembly length set to: 25
1771s Monitor turned on, set to: 1
1771s double stranded mode set
1771s min entropy set to: 1
1771s setting number of threads to: 2
1771s -setting parallel iworm mode.
1771s -reading Kmer occurrences...
1771s 
1771s  done parsing 96295 Kmers, 96295 added, taking 0 seconds.
1771s 
1771s TIMING KMER_DB_BUILDING 0 s.
1771s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
1771s Pruned 474 kmers from catalog.
1771s 	Pruning time: 0 seconds = 0 minutes.
1771s 
1771s TIMING PRUNING 0 s.
1771s -populating the kmer seed candidate list.
1771s Kcounter hash size: 96295
1771s Processed 95821 non-zero abundance kmers in kcounter.
1771s -Not sorting list of kmers, given parallel mode in effect.
1771s -beginning inchworm contig assembly.
1771s Total kcounter hash size: 96295 vs. sorted list size: 95821
1771s num threads set to: 2
1771s Done opening file. tmp.iworm.fa.pid_91742.thread_0
1771s Done opening file. tmp.iworm.fa.pid_91742.thread_1
1771s 
1771s 	Iworm contig assembly time: 0 seconds = 0 minutes.
1771s 
1771s TIMING CONTIG_BUILDING 0 s.
1771s 
1771s TIMING PROG_RUNTIME 0 s.
1771s * [Mon Nov  4 14:27:17 2024] Running CMD: mv /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa.tmp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa
1771s Monday, November 4, 2024: 14:27:17	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa.finished
1771s --------------------------------------------------------
1771s -------------------- Chrysalis -------------------------
1771s -- (Contig Clustering & de Bruijn Graph Construction) --
1771s --------------------------------------------------------
1771s 
1771s inchworm_target: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
1771s bowtie_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
1771s chrysalis_reads_fa: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
1771s * [Mon Nov  4 14:27:17 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa 100 10 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100
1771s * [Mon Nov  4 14:27:17 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 1>/dev/null
1772s * [Mon Nov  4 14:27:18 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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm.bowtie.nameSorted.bam" 
1777s * [Mon Nov  4 14:27:23 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_scaffolds.txt
1778s * [Mon Nov  4 14:27:24 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt
1781s * [Mon Nov  4 14:27:27 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G  -k9,9gr /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt.sorted
1781s * [Mon Nov  4 14:27:27 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1781s * [Mon Nov  4 14:27:27 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.vWCmNc/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.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/GraphFromIwormFasta.out
1781s * [Mon Nov  4 14:27:27 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/bundled_iworm_contigs.fasta -min 200
1781s * [Mon Nov  4 14:27:27 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa -f /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.vWCmNc/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 
1786s * [Mon Nov  4 14:27:32 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/readsToComponents.out > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/readsToComponents.out.sort
1786s Monday, November 4, 2024: 14:27:32	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/read_partitions/Fb_0/CBin_0
1786s Monday, November 4, 2024: 14:27:32	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/partitioned_reads.files.list.ok
1786s Monday, November 4, 2024: 14:27:32	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.vWCmNc/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
1786s Monday, November 4, 2024: 14:27:32	CMD: touch recursive_trinity.cmds.ok
1786s Monday, November 4, 2024: 14:27:32	CMD: touch recursive_trinity.cmds.ok
1786s 
1786s 
1786s --------------------------------------------------------------------------------
1786s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1786s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1786s --------------------------------------------------------------------------------
1786s 
1786s Monday, November 4, 2024: 14:27:32	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
1786s Number of Commands: 17
1841s 
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.    
1841s 
1841s All commands completed successfully. :-)
1841s 
1841s 
1841s 
1841s ** Harvesting all assembled transcripts into a single multi-fasta file...
1841s 
1841s Monday, November 4, 2024: 14:28:27	CMD: find /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/Trinity.tmp
1841s * [Mon Nov  4 14:28:27 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa 2
1842s * [Mon Nov  4 14:28:28 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta
1842s Monday, November 4, 2024: 14:28:28	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta.gene_trans_map
1842s 
1842s 
1842s #############################################################################
1842s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta
1842s #############################################################################
1842s 
1842s 
1842s 
1842s 
1842s exit 0
1842s touch test_all
1842s make[1]: Leaving directory '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly'
1842s Running example in test_GenomeGuidedTrinity...
1842s make[1]: Entering directory '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity'
1842s ./run_genome-guided_Trinity_use_existing_bam.sh
1842s #!/bin/bash -ve
1842s 
1842s if [ -e top100k.Left.fq.gz ] && ! [ -e top100k.Left.fq ]
1842s then
1842s 	gunzip -c top100k.Left.fq.gz > top100k.Left.fq
1842s fi
1843s 
1843s if [ -e top100k.Right.fq.gz ] && ! [ -e top100k.Right.fq ]
1843s then
1843s 	gunzip -c top100k.Right.fq.gz > top100k.Right.fq
1843s fi
1843s 
1843s 
1843s 
1843s if [ -e top100k.genome.gz ] && ! [ -e top100k.genome ]
1843s then
1843s 	gunzip -c top100k.genome.gz > top100k.genome
1843s fi
1843s 
1843s 
1843s 
1843s $TRINITY_HOME/Trinity --genome_guided_max_intron 1000 --genome_guided_bam SP2.chr.bam --max_memory 2G  --output test_GG_use_bam_trinity_outdir
1843s 
1843s 
1843s      ______  ____   ____  ____   ____  ______  __ __
1843s     |      ||    \ |    ||    \ |    ||      ||  |  |
1843s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1843s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1843s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1843s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1843s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1843s 
1843s     Trinity-v2.15.1
1843s 
1843s 
1843s 
1843s Monday, November 4, 2024: 14:28:29	CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl SP2.chr.bam
1843s -appears to be a coordinate sorted bam file. ok.
1843s Monday, November 4, 2024: 14:28:29	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir
1843s 
1843s 
1843s ----------------------------------------------------------------------------------
1843s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1843s ----------------------------------------------------------------------------------
1843s 
1843s -found paired-end aligned read. Running in paired-end mode.
1843s Monday, November 4, 2024: 14:28:29	CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/SP2.chr.bam
1844s Monday, November 4, 2024: 14:28:30	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/SP2.chr.bam.norm_200.bam.ok
1844s Monday, November 4, 2024: 14:28:30	CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.vWCmNc/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 
1844s 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 
1844s -extracting read coordinates from SP2.chr.bam.norm_200.bam into SP2.chr.bam.norm_200.bam.read_coords
1844s 
1844s CMD: touch SP2.chr.bam.norm_200.bam.read_coords.ok
1844s 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
1845s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1845s 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
1845s 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
1845s 
[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
1845s 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
1845s CMD: touch SP2.chr.bam.norm_200.bam.minC1.gff.ok
1845s 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 
1845s // parsing paritions.
1845s 
[71]  -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/14_122.trinity.reads
1845s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/212_1291.trinity.reads
1845s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/1392_1648.trinity.reads
1845s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/1797_2125.trinity.reads
1845s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/2163_3611.trinity.reads
1845s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/3633_3710.trinity.reads
1845s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads
1845s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/4913_5681.trinity.reads
1845s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/9938_10435.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/11319_11903.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/12073_12996.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/13623_13950.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/14321_14565.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/15124_16713.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/16949_17135.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17151_17239.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17291_17395.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17403_17460.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17486_18615.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/18669_19255.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/19312_19749.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/19806_20057.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/25542_25904.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/27107_27961.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/29764_32484.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/33570_35223.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/35276_35333.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/35616_35657.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/35667_36204.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/40913_41816.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/42003_43278.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/43414_43636.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/45059_45550.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/45591_49924.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/50916_53857.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/54299_54404.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/56263_56322.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/56460_59191.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/59428_61023.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/64539_69762.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/71026_71306.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/71566_71786.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/72348_72436.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/73883_73950.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/76379_76542.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/77783_78299.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/79543_79626.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/80570_80778.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/81974_82231.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/85575_85999.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/90691_93939.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/95200_96973.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/98644_98711.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads
1846s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/99132_100027.trinity.reads
1846s CMD: touch Dir_SP2.chr.bam.norm_200.bam.minC1.gff.ok
1846s ##
1846s Done
1846s ##
1846s 
1846s Monday, November 4, 2024: 14:28:32	CMD: touch partitions.ok
1846s Monday, November 4, 2024: 14:28:32	CMD: find Dir_* -name '*reads' > read_files.list
1846s Monday, November 4, 2024: 14:28:32	CMD: touch read_files.list.ok
1846s Monday, November 4, 2024: 14:28:32	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
1846s Monday, November 4, 2024: 14:28:32	CMD: touch trinity_GG.cmds.ok
1846s Monday, November 4, 2024: 14:28:32	CMD: touch trinity_GG.cmds.ok
1846s 
1846s 
1846s --------------------------------------------------------------------------------
1846s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1846s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1846s --------------------------------------------------------------------------------
1846s 
1846s Monday, November 4, 2024: 14:28:32	CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -v -shuffle 
1846s Number of Commands: 37
1898s 
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.    
1898s 
1898s All commands completed successfully. :-)
1898s 
1898s Monday, November 4, 2024: 14:29:24	CMD: find Dir_*  -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta.tmp
1898s Monday, November 4, 2024: 14:29:24	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta.gene_trans_map
1898s 
1898s 
1898s Finished. See /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta for reconstructed transcripts
1898s 
1898s 
1898s asmsize=$(wc -c <"test_GG_use_bam_trinity_outdir/Trinity-GG.fasta")
1898s ok
1898s if [ $asmsize -le 50000 ]; then
1898s     echo "Error, test_GG_use_bam_trinity_outdir/Trinity-GG.fasta potentially incomplete"
1898s     exit 1
1898s else
1898s     echo "ok"
1898s     exit 0
1898s fi
1898s ./run_Schizo_TrinityGG_jaccard_clip.sh
1898s #!/bin/bash -ve
1898s 
1898s $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
1898s 
1898s 
1898s      ______  ____   ____  ____   ____  ______  __ __
1898s     |      ||    \ |    ||    \ |    ||      ||  |  |
1898s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1898s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1898s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1898s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1898s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1898s 
1898s     Trinity-v2.15.1
1898s 
1898s 
1898s 
1898s Monday, November 4, 2024: 14:29:24	CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl SP2.chr.bam
1898s -appears to be a coordinate sorted bam file. ok.
1898s Monday, November 4, 2024: 14:29:24	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir
1898s 
1898s 
1898s ----------------------------------------------------------------------------------
1898s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1898s ----------------------------------------------------------------------------------
1898s 
1898s -found paired-end aligned read. Running in paired-end mode.
1898s Monday, November 4, 2024: 14:29:24	CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/SP2.chr.bam
1898s Monday, November 4, 2024: 14:29:24	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam.ok
1898s Monday, November 4, 2024: 14:29:24	CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.vWCmNc/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 
1898s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam RF
1899s 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 
1899s 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 
1899s -extracting read coordinates from SP2.chr.bam.norm_200.bam.+.sam into SP2.chr.bam.norm_200.bam.+.sam.read_coords
1899s 
1899s -extracting read coordinates from SP2.chr.bam.norm_200.bam.-.sam into SP2.chr.bam.norm_200.bam.-.sam.read_coords
1899s 
1899s CMD: touch SP2.chr.bam.norm_200.bam.-.sam.read_coords.ok
1899s 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
1900s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1900s 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
1900s 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
1900s 
[1000 lines read]  scaff:7000000090838467 lend:6194  rend:6433     
[2000 lines read]  scaff:7000000090838467 lend:46308  rend:46696     
[3000 lines read]  scaff:7000000090838467 lend:59573  rend:59951     CMD: touch SP2.chr.bam.norm_200.bam.+.sam.read_coords.ok
1900s 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
1900s 
[4000 lines read]  scaff:7000000090838467 lend:60068  rend:60313     
[5000 lines read]  scaff:7000000090838467 lend:60602  rend:60807     CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1900s 
[6000 lines read]  scaff:7000000090838467 lend:65099  rend:65468     
[7000 lines read]  scaff:7000000090838467 lend:65621  rend:65957     
[8000 lines read]  scaff:7000000090838467 lend:66173  rend:66538     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
1900s 
[9000 lines read]  scaff:7000000090838467 lend:88962  rend:89278     CMD: touch SP2.chr.bam.norm_200.bam.-.sam.frag_coverage.wig.ok
1900s 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
1900s 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
1900s 
[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     CMD: touch SP2.chr.bam.norm_200.bam.-.sam.minC1.gff.ok
1900s 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 
1900s 
[5000 lines read]  scaff:7000000090838467 lend:30519  rend:30759     // parsing paritions.
1900s 
[73]  -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/14_122.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/1392_1648.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/1797_2125.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3633_3710.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/4913_5470.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5606_5681.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads
1900s 
[6000 lines read]  scaff:7000000090838467 lend:52660  rend:52989     
[7000 lines read]  scaff:7000000090838467 lend:56475  rend:56834     -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/7478_7778.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/11319_11575.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/13623_13950.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/16160_16227.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/16322_16713.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/16949_17135.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/18334_18615.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/18745_19255.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/19312_19749.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/19806_20057.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/21538_21869.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/25632_25904.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/28689_28755.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/28953_29020.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/35276_35333.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/35667_36050.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads
1900s 
[8000 lines read]  scaff:7000000090838467 lend:57224  rend:57489     -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/43050_43256.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/43414_43636.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads
1900s 
[9000 lines read]  scaff:7000000090838467 lend:67627  rend:67818     -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/52320_52590.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/52965_53480.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/54299_54404.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55029_55235.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55243_55272.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55367_55660.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55765_56138.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56263_56322.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads
1900s 
[10000 lines read]  scaff:7000000090838467 lend:68505  rend:68690     -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads
1900s 
[11000 lines read]  scaff:7000000090838467 lend:69245  rend:69544     
[12000 lines read]  scaff:7000000090838467 lend:82862  rend:83065     
[13000 lines read]  scaff:7000000090838467 lend:83622  rend:83842     -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/63225_63476.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads
1900s 
[14000 lines read]  scaff:7000000090838467 lend:84137  rend:84436     CMD: touch SP2.chr.bam.norm_200.bam.+.sam.frag_coverage.wig.ok
1900s 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
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/67085_67370.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/69270_69337.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/71566_71786.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/73883_73950.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/76379_76542.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/77783_78299.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80570_80778.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81974_82231.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/83425_83673.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/83688_83987.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/84011_84078.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/85575_85999.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads
1900s CMD: touch SP2.chr.bam.norm_200.bam.+.sam.minC1.gff.ok
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads
1900s 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 
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/98744_98781.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads
1900s CMD: touch Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff.ok
1900s // parsing paritions.
1900s 
[57]  -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/872_939.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/963_1208.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/2378_2430.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/3465_3611.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/3804_3872.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/5374_5664.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/9938_10435.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/11471_11903.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/14321_14565.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/18669_18911.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/25542_25867.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/27107_27395.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/27630_27959.trinity.reads
1900s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/31628_31881.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/31893_32259.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/35616_35657.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/35987_36204.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/40913_41123.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/41133_41404.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/45059_45550.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/46429_46482.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/59886_59966.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/60255_61023.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/64782_64821.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/65880_65925.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/71026_71306.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/72348_72436.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/79543_79626.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/88618_88826.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98644_98711.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99067_99099.trinity.reads
1901s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads
1901s CMD: touch Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff.ok
1901s ##
1901s Done
1901s ##
1901s 
1901s Monday, November 4, 2024: 14:29:27	CMD: touch partitions.ok
1901s Monday, November 4, 2024: 14:29:27	CMD: find Dir_* -name '*reads' > read_files.list
1901s Monday, November 4, 2024: 14:29:27	CMD: touch read_files.list.ok
1901s Monday, November 4, 2024: 14:29:27	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
1901s Monday, November 4, 2024: 14:29:27	CMD: touch trinity_GG.cmds.ok
1901s Monday, November 4, 2024: 14:29:27	CMD: touch trinity_GG.cmds.ok
1901s 
1901s 
1901s --------------------------------------------------------------------------------
1901s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1901s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1901s --------------------------------------------------------------------------------
1901s 
1901s Monday, November 4, 2024: 14:29:27	CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -v -shuffle 
1901s Number of Commands: 53
1901s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1901s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1901s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1901s bt2 index files: $VAR1 = [];
1901s Note - bowtie-build indices do not yet exist. Indexing genome now.
1901s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1901s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1901s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1901s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1901s bt2 index files: $VAR1 = [];
1901s Note - bowtie-build indices do not yet exist. Indexing genome now.
1901s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1902s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1902s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1902s 85 reads; of these:
1902s   85 (100.00%) were unpaired; of these:
1902s     3 (3.53%) aligned 0 times
1902s     82 (96.47%) aligned exactly 1 time
1902s     0 (0.00%) aligned >1 times
1902s 96.47% overall alignment rate
1902s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1902s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1902s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1902s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1902s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1902s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1902s 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
1902s 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 
1902s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1902s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1902s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1902s 
1902s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1902s 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
1902s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1902s 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
1902s 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 
1902s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1902s -processing jaccard pair sensor
1902s 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
1902s 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
1902s 1717 reads; of these:
1902s   1717 (100.00%) were unpaired; of these:
1902s     1 (0.06%) aligned 0 times
1902s     1511 (88.00%) aligned exactly 1 time
1902s     205 (11.94%) aligned >1 times
1902s 99.94% overall alignment rate
1902s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1902s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1902s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1902s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1902s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1902s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1902s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1902s 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
1902s 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 
1902s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1902s 
1902s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1902s 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
1902s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1902s 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
1902s 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 
1902s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1902s -processing jaccard pair sensor
1902s 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
1902s 
[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
1902s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1904s 
succeeded(1)   1.88679% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1904s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1904s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1904s bt2 index files: $VAR1 = [];
1904s Note - bowtie-build indices do not yet exist. Indexing genome now.
1904s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1904s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1904s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1905s 2128 reads; of these:
1905s   2128 (100.00%) were unpaired; of these:
1905s     6 (0.28%) aligned 0 times
1905s     1722 (80.92%) aligned exactly 1 time
1905s     400 (18.80%) aligned >1 times
1905s 99.72% overall alignment rate
1905s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1905s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1905s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1905s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1905s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1905s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1905s 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
1905s 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 
1905s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1905s 
1905s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1905s 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
1905s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1905s 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
1905s 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 
1905s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1905s -processing jaccard pair sensor
1905s 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
1905s 
[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
1905s 
succeeded(2)   3.77358% completed.    CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1905s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1905s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1905s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1905s bt2 index files: $VAR1 = [];
1905s Note - bowtie-build indices do not yet exist. Indexing genome now.
1905s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1906s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1906s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1906s 30 reads; of these:
1906s   30 (100.00%) were unpaired; of these:
1906s     0 (0.00%) aligned 0 times
1906s     18 (60.00%) aligned exactly 1 time
1906s     12 (40.00%) aligned >1 times
1906s 100.00% overall alignment rate
1906s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1906s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1906s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1906s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1906s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1906s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1906s 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
1906s 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 
1906s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1906s 
1906s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1906s 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
1906s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1906s 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
1906s 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 
1906s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1906s -processing jaccard pair sensor
1906s 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
1906s 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
1906s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1908s 
succeeded(3)   5.66038% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1908s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1908s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1908s bt2 index files: $VAR1 = [];
1908s Note - bowtie-build indices do not yet exist. Indexing genome now.
1908s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1908s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1908s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1908s 24 reads; of these:
1908s   24 (100.00%) were unpaired; of these:
1908s     1 (4.17%) aligned 0 times
1908s     23 (95.83%) aligned exactly 1 time
1908s     0 (0.00%) aligned >1 times
1908s 95.83% overall alignment rate
1908s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1908s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1908s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1908s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1908s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1908s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1908s 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
1908s 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 
1908s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1908s 
1908s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1908s 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
1908s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1908s 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
1908s 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 
1908s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1908s -processing jaccard pair sensor
1908s 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
1908s 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
1908s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1909s 
succeeded(4)   7.54717% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1909s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1909s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1909s bt2 index files: $VAR1 = [];
1909s Note - bowtie-build indices do not yet exist. Indexing genome now.
1909s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1909s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1909s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1909s 309 reads; of these:
1909s   309 (100.00%) were unpaired; of these:
1909s     3 (0.97%) aligned 0 times
1909s     201 (65.05%) aligned exactly 1 time
1909s     105 (33.98%) aligned >1 times
1909s 99.03% overall alignment rate
1909s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1909s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1909s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1909s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1909s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1909s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1909s 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
1909s 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 
1909s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1909s 
1909s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1909s 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
1909s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1909s 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
1909s 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 
1909s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1909s -processing jaccard pair sensor
1909s 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
1909s 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
1909s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1910s 
succeeded(5)   9.43396% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1910s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1910s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1910s bt2 index files: $VAR1 = [];
1910s Note - bowtie-build indices do not yet exist. Indexing genome now.
1910s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1910s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1910s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1911s 213 reads; of these:
1911s   213 (100.00%) were unpaired; of these:
1911s     1 (0.47%) aligned 0 times
1911s     121 (56.81%) aligned exactly 1 time
1911s     91 (42.72%) aligned >1 times
1911s 99.53% overall alignment rate
1911s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1911s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1911s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1911s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1911s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1911s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1911s 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
1911s 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 
1911s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1911s 
1911s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1911s 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
1911s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1911s 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
1911s 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 
1911s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1911s -processing jaccard pair sensor
1911s 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
1911s 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
1911s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1912s 
succeeded(6)   11.3208% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1912s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1912s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1912s bt2 index files: $VAR1 = [];
1912s Note - bowtie-build indices do not yet exist. Indexing genome now.
1912s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1912s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1912s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1912s 10 reads; of these:
1912s   10 (100.00%) were unpaired; of these:
1912s     2 (20.00%) aligned 0 times
1912s     8 (80.00%) aligned exactly 1 time
1912s     0 (0.00%) aligned >1 times
1912s 80.00% overall alignment rate
1912s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1912s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1912s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1912s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1912s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1912s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1912s 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
1912s 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 
1912s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1912s 
1912s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1912s 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
1912s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1912s 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
1912s 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 
1912s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1912s -processing jaccard pair sensor
1912s 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
1912s 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
1912s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1913s 
succeeded(7)   13.2075% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1913s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1913s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1913s bt2 index files: $VAR1 = [];
1913s Note - bowtie-build indices do not yet exist. Indexing genome now.
1913s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s 
succeeded(8)   15.0943% completed.    CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1914s 10 reads; of these:
1914s   10 (100.00%) were unpaired; of these:
1914s     7 (70.00%) aligned 0 times
1914s     3 (30.00%) aligned exactly 1 time
1914s     0 (0.00%) aligned >1 times
1914s 30.00% overall alignment rate
1914s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1914s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s 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
1914s 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 
1914s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s bt2 index files: $VAR1 = [];
1914s Note - bowtie-build indices do not yet exist. Indexing genome now.
1914s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1914s 
1914s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1914s 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
1914s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s 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
1914s 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 
1914s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1914s -processing jaccard pair sensor
1914s 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
1914s 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
1914s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1914s 277 reads; of these:
1914s   277 (100.00%) were unpaired; of these:
1914s     0 (0.00%) aligned 0 times
1914s     277 (100.00%) aligned exactly 1 time
1914s     0 (0.00%) aligned >1 times
1914s 100.00% overall alignment rate
1914s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s 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
1914s 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 
1914s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1914s 
1914s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1914s 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
1914s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1914s 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
1914s 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 
1914s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1914s -processing jaccard pair sensor
1914s 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
1914s 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
1914s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1915s 
succeeded(9)   16.9811% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1915s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1915s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1915s bt2 index files: $VAR1 = [];
1915s Note - bowtie-build indices do not yet exist. Indexing genome now.
1915s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1915s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1915s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1915s 30 reads; of these:
1915s   30 (100.00%) were unpaired; of these:
1915s     9 (30.00%) aligned 0 times
1915s     21 (70.00%) aligned exactly 1 time
1915s     0 (0.00%) aligned >1 times
1915s 70.00% overall alignment rate
1915s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1915s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1915s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1915s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1915s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1915s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1915s 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
1915s 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 
1915s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1915s 
1915s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1915s 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
1915s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1915s 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
1915s 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 
1916s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1916s -processing jaccard pair sensor
1916s 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
1916s 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
1916s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1916s 
succeeded(10)   18.8679% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1916s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1916s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1916s bt2 index files: $VAR1 = [];
1916s Note - bowtie-build indices do not yet exist. Indexing genome now.
1916s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s 
succeeded(11)   20.7547% completed.    CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1917s 51 reads; of these:
1917s   51 (100.00%) were unpaired; of these:
1917s     4 (7.84%) aligned 0 times
1917s     47 (92.16%) aligned exactly 1 time
1917s     0 (0.00%) aligned >1 times
1917s 92.16% overall alignment rate
1917s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s 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
1917s 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 
1917s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1917s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1917s 
1917s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1917s 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
1917s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s 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
1917s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s 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 
1917s bt2 index files: $VAR1 = [];
1917s Note - bowtie-build indices do not yet exist. Indexing genome now.
1917s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1917s -processing jaccard pair sensor
1917s 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
1917s 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
1917s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1917s 454 reads; of these:
1917s   454 (100.00%) were unpaired; of these:
1917s     1 (0.22%) aligned 0 times
1917s     368 (81.06%) aligned exactly 1 time
1917s     85 (18.72%) aligned >1 times
1917s 99.78% overall alignment rate
1917s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s 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
1917s 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 
1917s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1917s 
1917s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1917s 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
1917s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1917s 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
1917s 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 
1917s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1917s -processing jaccard pair sensor
1917s 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
1917s 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
1917s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1919s 
succeeded(12)   22.6415% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1919s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1919s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1919s bt2 index files: $VAR1 = [];
1919s Note - bowtie-build indices do not yet exist. Indexing genome now.
1919s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1920s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1920s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1920s 
succeeded(13)   24.5283% completed.    2557 reads; of these:
1920s   2557 (100.00%) were unpaired; of these:
1920s     11 (0.43%) aligned 0 times
1920s     1332 (52.09%) aligned exactly 1 time
1920s     1214 (47.48%) aligned >1 times
1920s 99.57% overall alignment rate
1920s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1920s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1920s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1920s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1920s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1920s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1920s 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
1920s 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 
1920s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1920s 
1920s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1920s 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
1920s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1920s 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
1920s 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 
1920s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1920s -processing jaccard pair sensor
1920s 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
1920s 
[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
1920s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1920s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1920s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1920s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1921s bt2 index files: $VAR1 = [];
1921s Note - bowtie-build indices do not yet exist. Indexing genome now.
1921s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1921s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1921s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1921s 7038 reads; of these:
1921s   7038 (100.00%) were unpaired; of these:
1921s     25 (0.36%) aligned 0 times
1921s     2368 (33.65%) aligned exactly 1 time
1921s     4645 (66.00%) aligned >1 times
1921s 99.64% overall alignment rate
1922s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1922s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1922s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1922s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1922s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1922s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1922s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1922s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1922s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1922s 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
1922s 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 
1922s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1922s 
1923s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1923s 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
1923s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1923s 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
1923s 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 
1923s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1923s -processing jaccard pair sensor
1923s 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
1923s 
[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
1923s 
succeeded(14)   26.4151% completed.    CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1924s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1924s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1924s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1924s bt2 index files: $VAR1 = [];
1924s Note - bowtie-build indices do not yet exist. Indexing genome now.
1924s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1924s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1924s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1924s 77 reads; of these:
1924s   77 (100.00%) were unpaired; of these:
1924s     2 (2.60%) aligned 0 times
1924s     75 (97.40%) aligned exactly 1 time
1924s     0 (0.00%) aligned >1 times
1924s 97.40% overall alignment rate
1924s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1924s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1924s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1924s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1924s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1924s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1924s 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
1924s 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 
1924s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1924s 
1924s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1924s 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
1924s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1924s 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
1924s 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 
1924s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1924s -processing jaccard pair sensor
1924s 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
1924s 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
1924s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1928s 
succeeded(15)   28.3019% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1928s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1928s 
succeeded(16)   30.1887% completed.    CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1928s bt2 index files: $VAR1 = [];
1928s Note - bowtie-build indices do not yet exist. Indexing genome now.
1928s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1928s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1928s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1928s 5953 reads; of these:
1928s   5953 (100.00%) were unpaired; of these:
1928s     11 (0.18%) aligned 0 times
1928s     3807 (63.95%) aligned exactly 1 time
1928s     2135 (35.86%) aligned >1 times
1928s 99.82% overall alignment rate
1929s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1929s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1929s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1929s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1929s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1929s bt2 index files: $VAR1 = [];
1929s Note - bowtie-build indices do not yet exist. Indexing genome now.
1929s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1929s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1929s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1929s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1929s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1929s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1929s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1929s 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
1929s 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 
1929s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1929s 
1929s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1929s 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
1929s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1929s 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
1929s 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 
1929s 5664 reads; of these:
1929s   5664 (100.00%) were unpaired; of these:
1929s     8 (0.14%) aligned 0 times
1929s     3217 (56.80%) aligned exactly 1 time
1929s     2439 (43.06%) aligned >1 times
1929s 99.86% overall alignment rate
1929s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1929s -processing jaccard pair sensor
1929s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1929s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1930s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1930s 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
1930s 
[1000 lines read]  scaff:a1;90 lend:143  rend:454     
[2000 lines read]  scaff:a1;90 lend:1115  rend:1442     CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1930s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1930s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1930s 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
1930s 
[3000 lines read]  scaff:a1;90 lend:1905  rend:2258     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 
1930s 
[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
1930s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1930s 
1930s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1930s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1930s 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
1930s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1930s 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
1930s 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 
1930s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1930s -processing jaccard pair sensor
1930s 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
1931s 
[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
1931s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1935s 
succeeded(17)   32.0755% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1935s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1935s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1935s bt2 index files: $VAR1 = [];
1935s Note - bowtie-build indices do not yet exist. Indexing genome now.
1935s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1935s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1935s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1935s 24 reads; of these:
1935s   24 (100.00%) were unpaired; of these:
1935s     3 (12.50%) aligned 0 times
1935s     21 (87.50%) aligned exactly 1 time
1935s     0 (0.00%) aligned >1 times
1935s 87.50% overall alignment rate
1935s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1935s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1935s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1935s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1935s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1935s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1935s 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
1935s 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 
1935s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1935s 
1935s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1935s 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
1935s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1935s 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
1935s 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 
1935s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1935s -processing jaccard pair sensor
1935s 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
1935s 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
1935s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1936s 
succeeded(18)   33.9623% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1936s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1936s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1936s bt2 index files: $VAR1 = [];
1936s Note - bowtie-build indices do not yet exist. Indexing genome now.
1936s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1936s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1936s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1937s 1733 reads; of these:
1937s   1733 (100.00%) were unpaired; of these:
1937s     0 (0.00%) aligned 0 times
1937s     794 (45.82%) aligned exactly 1 time
1937s     939 (54.18%) aligned >1 times
1937s 100.00% overall alignment rate
1937s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1937s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1937s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1937s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1937s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1937s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1937s 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
1937s 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 
1937s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1937s 
1937s 
succeeded(19)   35.8491% completed.    CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1937s 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
1937s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1937s 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
1937s 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 
1937s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1937s -processing jaccard pair sensor
1937s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1937s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1937s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1937s 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
1937s bt2 index files: $VAR1 = [];
1937s Note - bowtie-build indices do not yet exist. Indexing genome now.
1937s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1937s 
[1000 lines read]  scaff:a22;2 lend:1  rend:49     
[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
1937s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1937s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1937s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1937s 115 reads; of these:
1937s   115 (100.00%) were unpaired; of these:
1937s     6 (5.22%) aligned 0 times
1937s     109 (94.78%) aligned exactly 1 time
1937s     0 (0.00%) aligned >1 times
1937s 94.78% overall alignment rate
1937s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1937s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1937s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1937s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1937s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1937s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1937s 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
1937s 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 
1937s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1937s 
1937s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1937s 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
1937s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1938s 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
1938s 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 
1938s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1938s -processing jaccard pair sensor
1938s 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
1938s 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
1938s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s 
succeeded(20)   37.7359% completed.    
succeeded(21)   39.6226% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1940s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s bt2 index files: $VAR1 = [];
1940s Note - bowtie-build indices do not yet exist. Indexing genome now.
1940s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1940s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s bt2 index files: $VAR1 = [];
1940s Note - bowtie-build indices do not yet exist. Indexing genome now.
1940s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1940s 20 reads; of these:
1940s   20 (100.00%) were unpaired; of these:
1940s     12 (60.00%) aligned 0 times
1940s     8 (40.00%) aligned exactly 1 time
1940s     0 (0.00%) aligned >1 times
1940s 40.00% overall alignment rate
1940s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s 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
1940s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1940s 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 
1940s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1940s 
1940s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1940s 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
1940s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s 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
1940s 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 
1940s 34 reads; of these:
1940s   34 (100.00%) were unpaired; of these:
1940s     1 (2.94%) aligned 0 times
1940s     33 (97.06%) aligned exactly 1 time
1940s     0 (0.00%) aligned >1 times
1940s 97.06% overall alignment rate
1940s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1940s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s -processing jaccard pair sensor
1940s 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
1940s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s 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
1940s 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
1940s 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 
1940s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1940s 
1940s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1940s 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
1940s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1940s 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
1940s 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 
1940s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1940s -processing jaccard pair sensor
1940s 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
1940s 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
1940s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1941s 
succeeded(22)   41.5094% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1941s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1941s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s bt2 index files: $VAR1 = [];
1942s Note - bowtie-build indices do not yet exist. Indexing genome now.
1942s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s 
succeeded(23)   43.3962% completed.    CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1942s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1942s 997 reads; of these:
1942s   997 (100.00%) were unpaired; of these:
1942s     3 (0.30%) aligned 0 times
1942s     568 (56.97%) aligned exactly 1 time
1942s     426 (42.73%) aligned >1 times
1942s 99.70% overall alignment rate
1942s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s bt2 index files: $VAR1 = [];
1942s Note - bowtie-build indices do not yet exist. Indexing genome now.
1942s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s 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
1942s 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 
1942s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1942s 
1942s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1942s 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
1942s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s 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
1942s 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 
1942s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1942s -processing jaccard pair sensor
1942s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1942s 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
1942s 70 reads; of these:
1942s   70 (100.00%) were unpaired; of these:
1942s     10 (14.29%) aligned 0 times
1942s     59 (84.29%) aligned exactly 1 time
1942s     1 (1.43%) aligned >1 times
1942s 85.71% overall alignment rate
1942s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s 
[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
1942s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s 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
1942s 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 
1942s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1942s 
1942s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1942s 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
1942s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1942s 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
1942s 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 
1942s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1942s -processing jaccard pair sensor
1942s 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
1942s 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
1942s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1945s 
succeeded(24)   45.283% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1945s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1945s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1945s bt2 index files: $VAR1 = [];
1945s Note - bowtie-build indices do not yet exist. Indexing genome now.
1945s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s 
succeeded(25)   47.1698% completed.    CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1946s 10 reads; of these:
1946s   10 (100.00%) were unpaired; of these:
1946s     3 (30.00%) aligned 0 times
1946s     7 (70.00%) aligned exactly 1 time
1946s     0 (0.00%) aligned >1 times
1946s 70.00% overall alignment rate
1946s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s 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
1946s 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 
1946s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1946s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1946s 
1946s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1946s 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
1946s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s 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
1946s 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 
1946s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s bt2 index files: $VAR1 = [];
1946s Note - bowtie-build indices do not yet exist. Indexing genome now.
1946s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1946s -processing jaccard pair sensor
1946s 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
1946s 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
1946s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1946s 293 reads; of these:
1946s   293 (100.00%) were unpaired; of these:
1946s     0 (0.00%) aligned 0 times
1946s     293 (100.00%) aligned exactly 1 time
1946s     0 (0.00%) aligned >1 times
1946s 100.00% overall alignment rate
1946s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s 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
1946s 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 
1946s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1946s 
1946s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1946s 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
1946s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1946s 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
1946s 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 
1946s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1946s -processing jaccard pair sensor
1946s 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
1946s 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
1946s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1947s 
succeeded(26)   49.0566% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1947s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1947s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1947s bt2 index files: $VAR1 = [];
1947s Note - bowtie-build indices do not yet exist. Indexing genome now.
1947s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1947s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1947s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1947s 26 reads; of these:
1947s   26 (100.00%) were unpaired; of these:
1947s     6 (23.08%) aligned 0 times
1947s     20 (76.92%) aligned exactly 1 time
1947s     0 (0.00%) aligned >1 times
1947s 76.92% overall alignment rate
1947s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1947s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1947s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1947s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1947s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1947s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1947s 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
1947s 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 
1947s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1947s 
1947s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1947s 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
1947s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1947s 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
1947s 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 
1947s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1947s -processing jaccard pair sensor
1947s 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
1947s 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
1947s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1949s 
succeeded(27)   50.9434% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1949s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1949s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1949s bt2 index files: $VAR1 = [];
1949s Note - bowtie-build indices do not yet exist. Indexing genome now.
1949s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1949s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1949s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1949s 54 reads; of these:
1949s   54 (100.00%) were unpaired; of these:
1949s     9 (16.67%) aligned 0 times
1949s     45 (83.33%) aligned exactly 1 time
1949s     0 (0.00%) aligned >1 times
1949s 83.33% overall alignment rate
1949s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1949s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1949s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1949s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1949s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1949s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1949s 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
1949s 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 
1949s 
succeeded(28)   52.8302% completed.    -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1949s 
1949s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1949s 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
1949s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1949s 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
1949s 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 
1949s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1949s -processing jaccard pair sensor
1949s 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
1949s 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
1949s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1949s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1949s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1949s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1949s bt2 index files: $VAR1 = [];
1949s Note - bowtie-build indices do not yet exist. Indexing genome now.
1949s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1950s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1950s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1950s 145 reads; of these:
1950s   145 (100.00%) were unpaired; of these:
1950s     1 (0.69%) aligned 0 times
1950s     144 (99.31%) aligned exactly 1 time
1950s     0 (0.00%) aligned >1 times
1950s 99.31% overall alignment rate
1950s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1950s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1950s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1950s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1950s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1950s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1950s 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
1950s 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 
1950s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1950s 
1950s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1950s 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
1950s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1950s 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
1950s 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 
1950s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1950s -processing jaccard pair sensor
1950s 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
1950s 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
1950s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1951s 
succeeded(29)   54.717% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1951s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1951s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1951s bt2 index files: $VAR1 = [];
1951s Note - bowtie-build indices do not yet exist. Indexing genome now.
1951s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1951s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1951s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1951s 16 reads; of these:
1951s   16 (100.00%) were unpaired; of these:
1951s     10 (62.50%) aligned 0 times
1951s     6 (37.50%) aligned exactly 1 time
1951s     0 (0.00%) aligned >1 times
1951s 37.50% overall alignment rate
1951s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1951s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1951s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1951s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1951s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1951s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1951s 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
1951s 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 
1951s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1951s 
1951s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1951s 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
1951s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1951s 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
1951s 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 
1951s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1951s -processing jaccard pair sensor
1951s 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
1951s 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
1951s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1952s 
succeeded(30)   56.6038% completed.    
succeeded(31)   58.4906% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1952s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1952s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1952s bt2 index files: $VAR1 = [];
1952s Note - bowtie-build indices do not yet exist. Indexing genome now.
1952s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1952s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1952s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1952s 818 reads; of these:
1952s   818 (100.00%) were unpaired; of these:
1952s     1 (0.12%) aligned 0 times
1952s     758 (92.67%) aligned exactly 1 time
1952s     59 (7.21%) aligned >1 times
1952s 99.88% overall alignment rate
1952s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1952s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1953s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s 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
1953s 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 
1953s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s bt2 index files: $VAR1 = [];
1953s Note - bowtie-build indices do not yet exist. Indexing genome now.
1953s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1953s 
1953s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1953s 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
1953s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s 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
1953s 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 
1953s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1953s -processing jaccard pair sensor
1953s 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
1953s 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
1953s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1953s 3962 reads; of these:
1953s   3962 (100.00%) were unpaired; of these:
1953s     2 (0.05%) aligned 0 times
1953s     2253 (56.87%) aligned exactly 1 time
1953s     1707 (43.08%) aligned >1 times
1953s 99.95% overall alignment rate
1953s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1953s 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
1953s 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 
1953s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1953s 
1954s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1954s 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
1954s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1954s 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
1954s 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 
1954s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1954s -processing jaccard pair sensor
1954s 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
1954s 
[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
1954s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1956s 
succeeded(32)   60.3774% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1956s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1956s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1956s bt2 index files: $VAR1 = [];
1956s Note - bowtie-build indices do not yet exist. Indexing genome now.
1956s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1956s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1956s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1956s 26 reads; of these:
1956s   26 (100.00%) were unpaired; of these:
1956s     0 (0.00%) aligned 0 times
1956s     26 (100.00%) aligned exactly 1 time
1956s     0 (0.00%) aligned >1 times
1956s 100.00% overall alignment rate
1956s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1956s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1956s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1956s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1956s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1956s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1956s 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
1956s 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 
1956s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1956s 
1956s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1956s 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
1956s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1956s 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
1956s 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 
1956s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1956s -processing jaccard pair sensor
1956s 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
1956s 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
1957s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1957s 
succeeded(33)   62.2641% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1957s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1957s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1957s bt2 index files: $VAR1 = [];
1957s Note - bowtie-build indices do not yet exist. Indexing genome now.
1957s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1958s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1958s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1958s 27 reads; of these:
1958s   27 (100.00%) were unpaired; of these:
1958s     6 (22.22%) aligned 0 times
1958s     21 (77.78%) aligned exactly 1 time
1958s     0 (0.00%) aligned >1 times
1958s 77.78% overall alignment rate
1958s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1958s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1958s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1958s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1958s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1958s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1958s 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
1958s 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 
1958s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1958s 
1958s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1958s 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
1958s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1958s 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
1958s 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 
1958s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1958s -processing jaccard pair sensor
1958s 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
1958s 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
1958s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1958s 
succeeded(34)   64.1509% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1958s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1959s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s bt2 index files: $VAR1 = [];
1959s Note - bowtie-build indices do not yet exist. Indexing genome now.
1959s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1959s 16 reads; of these:
1959s   16 (100.00%) were unpaired; of these:
1959s     0 (0.00%) aligned 0 times
1959s     14 (87.50%) aligned exactly 1 time
1959s     2 (12.50%) aligned >1 times
1959s 100.00% overall alignment rate
1959s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s 
succeeded(35)   66.0377% completed.    CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s 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
1959s 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 
1959s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1959s 
1959s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1959s 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
1959s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s 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
1959s 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 
1959s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1959s -processing jaccard pair sensor
1959s 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
1959s 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
1959s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1959s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s bt2 index files: $VAR1 = [];
1959s Note - bowtie-build indices do not yet exist. Indexing genome now.
1959s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1959s 371 reads; of these:
1959s   371 (100.00%) were unpaired; of these:
1959s     2 (0.54%) aligned 0 times
1959s     296 (79.78%) aligned exactly 1 time
1959s     73 (19.68%) aligned >1 times
1959s 99.46% overall alignment rate
1959s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1959s 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
1960s 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 
1960s 
succeeded(36)   67.9245% completed.    -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1960s 
1960s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1960s 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
1960s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1960s 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
1960s 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 
1960s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1960s -processing jaccard pair sensor
1960s 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
1960s 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
1960s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1960s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1960s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1960s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1960s bt2 index files: $VAR1 = [];
1960s Note - bowtie-build indices do not yet exist. Indexing genome now.
1960s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1960s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1960s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1960s 26 reads; of these:
1960s   26 (100.00%) were unpaired; of these:
1960s     17 (65.38%) aligned 0 times
1960s     9 (34.62%) aligned exactly 1 time
1960s     0 (0.00%) aligned >1 times
1960s 34.62% overall alignment rate
1960s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1960s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1960s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1960s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1960s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1960s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1960s 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
1960s 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 
1960s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1960s 
1960s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1960s 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
1960s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1960s 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
1960s 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 
1960s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1960s -processing jaccard pair sensor
1960s 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
1960s 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
1960s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s 
succeeded(37)   69.8113% completed.    
succeeded(38)   71.6981% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1962s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s bt2 index files: $VAR1 = [];
1962s Note - bowtie-build indices do not yet exist. Indexing genome now.
1962s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1962s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s bt2 index files: $VAR1 = [];
1962s Note - bowtie-build indices do not yet exist. Indexing genome now.
1962s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1962s 1811 reads; of these:
1962s   1811 (100.00%) were unpaired; of these:
1962s     6 (0.33%) aligned 0 times
1962s     1189 (65.65%) aligned exactly 1 time
1962s     616 (34.01%) aligned >1 times
1962s 99.67% overall alignment rate
1962s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1962s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s 52 reads; of these:
1962s   52 (100.00%) were unpaired; of these:
1962s     5 (9.62%) aligned 0 times
1962s     47 (90.38%) aligned exactly 1 time
1962s     0 (0.00%) aligned >1 times
1962s 90.38% overall alignment rate
1962s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s 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
1962s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s 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
1962s 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 
1962s 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 
1962s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1962s 
1962s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1962s 
1962s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1962s 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
1962s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s 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
1962s 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 
1962s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1962s -processing jaccard pair sensor
1962s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1962s 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
1962s 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
1962s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s 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
1962s 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
1962s 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 
1962s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1962s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1962s -processing jaccard pair sensor
1962s 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
1962s 
[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
1962s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1965s 
succeeded(39)   73.5849% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1965s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1965s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1965s bt2 index files: $VAR1 = [];
1965s Note - bowtie-build indices do not yet exist. Indexing genome now.
1965s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1965s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1965s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1965s 
succeeded(40)   75.4717% completed.    538 reads; of these:
1965s   538 (100.00%) were unpaired; of these:
1965s     2 (0.37%) aligned 0 times
1965s     530 (98.51%) aligned exactly 1 time
1965s     6 (1.12%) aligned >1 times
1965s 99.63% overall alignment rate
1965s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1965s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1965s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1965s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1965s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1965s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1965s 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
1965s 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 
1965s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1965s 
1965s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1965s 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
1965s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1965s 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
1965s 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 
1965s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1965s -processing jaccard pair sensor
1965s 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
1965s 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
1965s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1965s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1965s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1965s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1965s bt2 index files: $VAR1 = [];
1965s Note - bowtie-build indices do not yet exist. Indexing genome now.
1965s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1966s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1966s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1966s 907 reads; of these:
1966s   907 (100.00%) were unpaired; of these:
1966s     2 (0.22%) aligned 0 times
1966s     839 (92.50%) aligned exactly 1 time
1966s     66 (7.28%) aligned >1 times
1966s 99.78% overall alignment rate
1966s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1966s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1966s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1966s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1966s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1966s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1966s 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
1966s 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 
1966s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1966s 
1966s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1966s 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
1966s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1966s 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
1966s 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 
1966s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1966s -processing jaccard pair sensor
1966s 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
1966s 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
1966s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1968s 
succeeded(41)   77.3585% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1968s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1968s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1968s bt2 index files: $VAR1 = [];
1968s Note - bowtie-build indices do not yet exist. Indexing genome now.
1968s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1969s 
succeeded(42)   79.2453% completed.    18 reads; of these:
1969s   18 (100.00%) were unpaired; of these:
1969s     1 (5.56%) aligned 0 times
1969s     17 (94.44%) aligned exactly 1 time
1969s     0 (0.00%) aligned >1 times
1969s 94.44% overall alignment rate
1969s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s 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
1969s 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 
1969s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1969s 
1969s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1969s 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
1969s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s 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
1969s 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 
1969s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1969s -processing jaccard pair sensor
1969s 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
1969s 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
1969s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1969s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s bt2 index files: $VAR1 = [];
1969s Note - bowtie-build indices do not yet exist. Indexing genome now.
1969s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1969s 18 reads; of these:
1969s   18 (100.00%) were unpaired; of these:
1969s     5 (27.78%) aligned 0 times
1969s     13 (72.22%) aligned exactly 1 time
1969s     0 (0.00%) aligned >1 times
1969s 72.22% overall alignment rate
1969s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s 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
1969s 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 
1969s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1969s 
1969s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1969s 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
1969s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1969s 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
1969s 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 
1969s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1969s -processing jaccard pair sensor
1969s 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
1969s 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
1969s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1970s 
succeeded(43)   81.1321% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1970s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1970s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1970s bt2 index files: $VAR1 = [];
1970s Note - bowtie-build indices do not yet exist. Indexing genome now.
1970s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s 
succeeded(44)   83.0189% completed.    CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1971s 76 reads; of these:
1971s   76 (100.00%) were unpaired; of these:
1971s     0 (0.00%) aligned 0 times
1971s     76 (100.00%) aligned exactly 1 time
1971s     0 (0.00%) aligned >1 times
1971s 100.00% overall alignment rate
1971s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1971s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s 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
1971s 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 
1971s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s bt2 index files: $VAR1 = [];
1971s Note - bowtie-build indices do not yet exist. Indexing genome now.
1971s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1971s 
1971s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1971s 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
1971s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s 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
1971s 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 
1971s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1971s -processing jaccard pair sensor
1971s 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
1971s 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
1971s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1971s 42 reads; of these:
1971s   42 (100.00%) were unpaired; of these:
1971s     18 (42.86%) aligned 0 times
1971s     24 (57.14%) aligned exactly 1 time
1971s     0 (0.00%) aligned >1 times
1971s 57.14% overall alignment rate
1971s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s 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
1971s 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 
1971s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1971s 
1971s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1971s 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
1971s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1971s 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
1971s 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 
1971s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1971s -processing jaccard pair sensor
1971s 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
1971s 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
1971s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1973s 
succeeded(45)   84.9057% completed.    
succeeded(46)   86.7924% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1973s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1973s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1973s bt2 index files: $VAR1 = [];
1973s Note - bowtie-build indices do not yet exist. Indexing genome now.
1973s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1973s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1973s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1973s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1973s bt2 index files: $VAR1 = [];
1973s Note - bowtie-build indices do not yet exist. Indexing genome now.
1973s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1973s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1973s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1973s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1973s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1973s 4380 reads; of these:
1973s   4380 (100.00%) were unpaired; of these:
1973s     10 (0.23%) aligned 0 times
1973s     2462 (56.21%) aligned exactly 1 time
1973s     1908 (43.56%) aligned >1 times
1973s 99.77% overall alignment rate
1973s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1973s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1973s 953 reads; of these:
1973s   953 (100.00%) were unpaired; of these:
1973s     4 (0.42%) aligned 0 times
1973s     555 (58.24%) aligned exactly 1 time
1973s     394 (41.34%) aligned >1 times
1973s 99.58% overall alignment rate
1973s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1973s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1974s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1974s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1974s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1974s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1974s 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
1974s 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 
1974s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1974s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1974s 
1974s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1974s 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
1974s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1974s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1974s 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
1974s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1974s 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 
1974s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1974s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1974s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1974s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1974s 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
1974s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1974s -processing jaccard pair sensor
1974s 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 
1974s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1974s 
1974s 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
1974s 
[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
1974s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1974s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1974s 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
1974s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1974s 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
1974s 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 
1974s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1974s -processing jaccard pair sensor
1974s 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
1974s 
[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
1974s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1977s 
succeeded(47)   88.6792% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1977s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1977s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1977s bt2 index files: $VAR1 = [];
1977s Note - bowtie-build indices do not yet exist. Indexing genome now.
1977s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1978s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1978s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1978s 20 reads; of these:
1978s   20 (100.00%) were unpaired; of these:
1978s     4 (20.00%) aligned 0 times
1978s     16 (80.00%) aligned exactly 1 time
1978s     0 (0.00%) aligned >1 times
1978s 80.00% overall alignment rate
1978s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1978s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1978s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1978s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1978s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1978s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1978s 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
1978s 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 
1978s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1978s 
1978s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1978s 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
1978s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1978s 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
1978s 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 
1978s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1978s -processing jaccard pair sensor
1978s 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
1978s 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
1978s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1978s 
succeeded(48)   90.566% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1978s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1978s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1978s bt2 index files: $VAR1 = [];
1978s Note - bowtie-build indices do not yet exist. Indexing genome now.
1978s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1979s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1979s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1979s 98 reads; of these:
1979s   98 (100.00%) were unpaired; of these:
1979s     0 (0.00%) aligned 0 times
1979s     98 (100.00%) aligned exactly 1 time
1979s     0 (0.00%) aligned >1 times
1979s 100.00% overall alignment rate
1979s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1979s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1979s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1979s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1979s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1979s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1979s 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
1979s 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 
1979s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1979s 
1979s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1979s 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
1979s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1979s 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
1979s 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 
1979s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1979s -processing jaccard pair sensor
1979s 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
1979s 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
1979s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1979s 
succeeded(49)   92.4528% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1979s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1979s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1979s bt2 index files: $VAR1 = [];
1979s Note - bowtie-build indices do not yet exist. Indexing genome now.
1979s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1980s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1980s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1980s 85 reads; of these:
1980s   85 (100.00%) were unpaired; of these:
1980s     6 (7.06%) aligned 0 times
1980s     79 (92.94%) aligned exactly 1 time
1980s     0 (0.00%) aligned >1 times
1980s 92.94% overall alignment rate
1980s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1980s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1980s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1980s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1980s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1980s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1980s 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
1980s 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 
1980s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1980s 
1980s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1980s 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
1980s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1980s 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
1980s 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 
1980s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1980s -processing jaccard pair sensor
1980s 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
1980s 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
1980s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1981s 
succeeded(50)   94.3396% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1981s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1981s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1981s bt2 index files: $VAR1 = [];
1981s Note - bowtie-build indices do not yet exist. Indexing genome now.
1981s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1981s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1981s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1981s 10 reads; of these:
1981s   10 (100.00%) were unpaired; of these:
1981s     5 (50.00%) aligned 0 times
1981s     5 (50.00%) aligned exactly 1 time
1981s     0 (0.00%) aligned >1 times
1981s 50.00% overall alignment rate
1981s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1981s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1981s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1981s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1981s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1981s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1981s 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
1981s 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 
1981s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1981s 
1981s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1981s 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
1981s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1981s 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
1981s 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 
1981s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1981s -processing jaccard pair sensor
1981s 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
1981s 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
1982s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1982s 
succeeded(51)   96.2264% completed.    CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1982s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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 
1982s CMD: samtools faidx /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1982s bt2 index files: $VAR1 = [];
1982s Note - bowtie-build indices do not yet exist. Indexing genome now.
1982s CMD: bowtie2-build -q /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1982s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1982s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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" 
1982s 
succeeded(52)   98.1132% completed.    46 reads; of these:
1982s   46 (100.00%) were unpaired; of these:
1982s     0 (0.00%) aligned 0 times
1982s     44 (95.65%) aligned exactly 1 time
1982s     2 (4.35%) aligned >1 times
1982s 100.00% overall alignment rate
1982s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1982s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1982s CMD: samtools view -bt /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1982s CMD: samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1982s -cleaning up and removing intermediate file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1982s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1982s 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
1982s 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 
1983s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1983s 
1983s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1983s 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
1983s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1983s 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
1983s 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 
1983s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1983s -processing jaccard pair sensor
1983s 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
1983s 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
1983s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/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
1984s 
succeeded(53)   100% completed.    
1984s 
1984s All commands completed successfully. :-)
1984s 
1984s Monday, November 4, 2024: 14:30:50	CMD: find Dir_*  -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta.tmp
1984s Monday, November 4, 2024: 14:30:50	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta.gene_trans_map
1984s 
1984s 
1984s Finished. See /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta for reconstructed transcripts
1984s 
1984s 
1984s outfile="test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta"
1984s asmsize=$(wc -c <"${outfile}")
1984s if [ $asmsize -le 50000 ]; then
1984s     echo "Error, ${outfile} potentially incomplete"
1984s     exit 1
1984s else
1984s ok
1984s ./run_small_GG_mutliScaff_test.sh
1984s     echo "ok"
1984s     exit 0
1984s fi
1984s #!/bin/bash -ve
1984s 
1984s 
1984s $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
1984s 
1984s 
1984s      ______  ____   ____  ____   ____  ______  __ __
1984s     |      ||    \ |    ||    \ |    ||      ||  |  |
1984s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1984s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1984s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1984s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1984s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1984s 
1984s     Trinity-v2.15.1
1984s 
1984s 
1984s 
1984s Monday, November 4, 2024: 14:30:50	CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl transAligns.cSorted.bam
1984s -appears to be a coordinate sorted bam file. ok.
1984s Monday, November 4, 2024: 14:30:50	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir
1984s 
1984s 
1984s ----------------------------------------------------------------------------------
1984s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1984s ----------------------------------------------------------------------------------
1984s 
1984s -found paired-end aligned read. Running in paired-end mode.
1984s Monday, November 4, 2024: 14:30:50	CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/transAligns.cSorted.bam
1987s Done with chr TRINITY_DN0_c0_g1_i1.
1987s Done with chr TRINITY_DN10_c0_g1_i1.
1987s Done with chr TRINITY_DN12_c0_g1_i1.
1987s Done with chr TRINITY_DN12_c0_g1_i2.
1987s Done with chr TRINITY_DN14_c0_g1_i1.
1987s Done with chr TRINITY_DN14_c0_g2_i1.
1987s Done with chr TRINITY_DN15_c0_g1_i1.
1987s Done with chr TRINITY_DN16_c0_g1_i1.
1987s Done with chr TRINITY_DN16_c0_g2_i1.
1987s Done with chr TRINITY_DN18_c0_g1_i1.
1987s Done with chr TRINITY_DN18_c0_g1_i2.
1987s Done with chr TRINITY_DN19_c0_g1_i1.
1987s Done with chr TRINITY_DN20_c0_g1_i1.
1987s Done with chr TRINITY_DN20_c0_g2_i1.
1987s Done with chr TRINITY_DN20_c0_g1_i2.
1987s Done with chr TRINITY_DN20_c0_g1_i3.
1987s Done with chr TRINITY_DN20_c0_g1_i4.
1987s Done with chr TRINITY_DN20_c0_g1_i5.
1987s Done with chr TRINITY_DN20_c0_g1_i6.
1987s Done with chr TRINITY_DN20_c0_g1_i7.
1987s Done with chr TRINITY_DN21_c0_g1_i1.
1987s Done with chr TRINITY_DN21_c0_g1_i2.
1987s Done with chr TRINITY_DN22_c0_g1_i1.
1987s Done with chr TRINITY_DN22_c0_g2_i1.
1987s Done with chr TRINITY_DN22_c0_g3_i1.
1987s Done with chr TRINITY_DN22_c0_g4_i1.
1987s Done with chr TRINITY_DN22_c0_g3_i2.
1987s Done with chr TRINITY_DN22_c0_g3_i3.
1987s Done with chr TRINITY_DN22_c0_g3_i4.
1987s Done with chr TRINITY_DN22_c0_g5_i1.
1987s Done with chr TRINITY_DN22_c0_g6_i1.
1987s Done with chr TRINITY_DN22_c0_g3_i5.
1987s Done with chr TRINITY_DN22_c0_g7_i1.
1987s Done with chr TRINITY_DN23_c0_g1_i1.
1987s Done with chr TRINITY_DN23_c0_g2_i1.
1987s Done with chr TRINITY_DN23_c0_g1_i2.
1987s Done with chr TRINITY_DN23_c0_g3_i1.
1987s Done with chr TRINITY_DN23_c0_g4_i1.
1987s Done with chr TRINITY_DN23_c0_g5_i1.
1987s Done with chr TRINITY_DN23_c0_g1_i3.
1987s Done with chr TRINITY_DN23_c0_g1_i4.
1987s Done with chr TRINITY_DN24_c0_g1_i1.
1987s Done with chr TRINITY_DN24_c0_g2_i1.
1987s Done with chr TRINITY_DN24_c0_g3_i1.
1987s Done with chr TRINITY_DN24_c0_g3_i2.
1987s Done with chr TRINITY_DN25_c1_g1_i1.
1987s Done with chr TRINITY_DN25_c1_g1_i2.
1987s Done with chr TRINITY_DN25_c1_g1_i3.
1987s Done with chr TRINITY_DN25_c1_g1_i4.
1987s Done with chr TRINITY_DN25_c1_g1_i5.
1987s Done with chr TRINITY_DN26_c0_g1_i1.
1987s Done with chr TRINITY_DN26_c0_g1_i2.
1987s Done with chr TRINITY_DN26_c1_g1_i1.
1987s Done with chr TRINITY_DN26_c1_g1_i2.
1987s Done with chr TRINITY_DN26_c1_g1_i3.
1987s Done with chr TRINITY_DN26_c1_g1_i4.
1987s Done with chr TRINITY_DN26_c1_g1_i5.
1987s Done with chr TRINITY_DN26_c1_g1_i6.
1987s Done with chr TRINITY_DN26_c1_g2_i1.
1987s Done with chr TRINITY_DN26_c1_g1_i7.
1987s Done with chr TRINITY_DN26_c1_g3_i1.
1987s Done with chr TRINITY_DN26_c1_g1_i8.
1987s Done with chr TRINITY_DN26_c1_g1_i9.
1987s Done with chr TRINITY_DN26_c1_g1_i10.
1987s Done with chr TRINITY_DN26_c1_g1_i11.
1987s Done with chr TRINITY_DN26_c1_g3_i2.
1987s Done with chr TRINITY_DN26_c1_g1_i12.
1987s Done with chr TRINITY_DN26_c1_g4_i1.
1987s Done with chr TRINITY_DN26_c1_g1_i13.
1987s Done with chr TRINITY_DN26_c1_g1_i14.
1987s Done with chr TRINITY_DN26_c1_g1_i15.
1987s Done with chr TRINITY_DN26_c1_g1_i16.
1987s Done with chr TRINITY_DN26_c1_g1_i17.
1987s Done with chr TRINITY_DN26_c1_g1_i18.
1987s Done with chr TRINITY_DN26_c1_g3_i3.
1987s Done with chr TRINITY_DN26_c1_g1_i19.
1987s Done with chr TRINITY_DN26_c1_g3_i4.
1987s Done with chr TRINITY_DN26_c1_g5_i1.
1987s Done with chr TRINITY_DN26_c1_g1_i20.
1987s Done with chr TRINITY_DN26_c1_g1_i21.
1987s Done with chr TRINITY_DN26_c1_g3_i5.
1987s Done with chr TRINITY_DN26_c2_g1_i1.
1987s Done with chr TRINITY_DN26_c2_g1_i2.
1987s Done with chr TRINITY_DN26_c2_g2_i1.
1987s Done with chr TRINITY_DN26_c2_g3_i1.
1987s Done with chr TRINITY_DN26_c2_g1_i3.
1987s Done with chr TRINITY_DN26_c2_g1_i4.
1987s Done with chr TRINITY_DN26_c2_g1_i5.
1987s Done with chr TRINITY_DN27_c0_g1_i1.
1987s Done with chr TRINITY_DN4_c0_g1_i1.
1987s Done with chr TRINITY_DN5_c0_g1_i1.
1987s Monday, November 4, 2024: 14:30:53	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/transAligns.cSorted.bam.norm_200.bam.ok
1987s Monday, November 4, 2024: 14:30:53	CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.vWCmNc/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 
1987s 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 
1987s -extracting read coordinates from transAligns.cSorted.bam.norm_200.bam into transAligns.cSorted.bam.norm_200.bam.read_coords
1987s 
1992s CMD: touch transAligns.cSorted.bam.norm_200.bam.read_coords.ok
1992s 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
1992s CMD: cp /tmp/autopkgtest.vWCmNc/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.vWCmNc/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
1993s 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
1993s 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
1997s 
[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
1997s 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
1997s CMD: touch transAligns.cSorted.bam.norm_200.bam.minC1.gff.ok
1997s 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 
1997s // parsing paritions.
1997s 
[92]  -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN0_c0_g1_i1/0/1_251.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN10_c0_g1_i1/0/1_307.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN12_c0_g1_i1/0/1_246.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN12_c0_g1_i2/0/1_312.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN14_c0_g1_i1/0/1_280.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN14_c0_g2_i1/0/1_390.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN15_c0_g1_i1/0/1_239.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN16_c0_g1_i1/0/1_272.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN16_c0_g2_i1/0/1_324.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN18_c0_g1_i1/0/36_344.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN18_c0_g1_i2/0/36_348.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN19_c0_g1_i1/0/1_304.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i1/0/1_769.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g2_i1/0/1_484.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i2/0/3_2306.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i3/0/1_2226.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i4/0/1_2619.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i5/0/1_1442.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i6/0/1_1946.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i7/0/1_2899.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN21_c0_g1_i1/0/1_2802.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN21_c0_g1_i2/0/1_3823.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g1_i1/0/1_422.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g2_i1/0/1_204.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i1/0/1_2433.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g4_i1/0/1_219.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i2/0/1_790.trinity.reads
1997s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i3/0/1_2269.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i4/0/1_2200.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g5_i1/0/1_590.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g6_i1/0/1_246.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i5/0/1_2364.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g7_i1/0/1_513.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i1/0/1_799.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g2_i1/0/1_205.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i2/0/1_2592.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g3_i1/0/1_289.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g4_i1/0/1_341.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g5_i1/0/1_952.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i3/0/1_2514.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i4/0/1_296.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g1_i1/0/1_205.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g2_i1/0/1_433.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g3_i1/0/3_7194.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g3_i2/0/2_530.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i1/0/1_1375.trinity.reads
1998s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i2/0/1_3516.trinity.reads
1999s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i3/0/1_3667.trinity.reads
1999s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i4/0/1_3625.trinity.reads
1999s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i5/0/1_220.trinity.reads
1999s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c0_g1_i1/0/1_5399.trinity.reads
1999s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c0_g1_i2/0/1_5528.trinity.reads
1999s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i1/0/1_8158.trinity.reads
1999s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i2/0/1_8134.trinity.reads
2000s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i3/0/1_8130.trinity.reads
2000s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i4/0/1_8138.trinity.reads
2000s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i5/0/1_8087.trinity.reads
2000s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i6/0/1_8146.trinity.reads
2000s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g2_i1/0/1_341.trinity.reads
2000s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i7/0/1_8091.trinity.reads
2000s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i1/0/1_5713.trinity.reads
2001s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i8/0/1_8079.trinity.reads
2001s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i9/0/1_8122.trinity.reads
2001s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i10/0/1_8150.trinity.reads
2001s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i11/0/1_6104.trinity.reads
2001s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i2/0/1_5905.trinity.reads
2001s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i12/0/1_8130.trinity.reads
2001s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g4_i1/0/1_298.trinity.reads
2001s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i13/0/1_8126.trinity.reads
2002s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i14/0/1_8091.trinity.reads
2002s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i15/0/1_8095.trinity.reads
2002s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i16/0/1_8150.trinity.reads
2002s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i17/0/1_8142.trinity.reads
2002s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i18/0/1_8099.trinity.reads
2002s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i3/0/1_3101.trinity.reads
2002s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i19/0/1_6546.trinity.reads
2003s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i4/0/1_5854.trinity.reads
2003s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g5_i1/0/1_215.trinity.reads
2003s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i20/0/1_8154.trinity.reads
2003s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i21/0/1_6129.trinity.reads
2003s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i5/0/1_3918.trinity.reads
2003s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i1/0/1_8817.trinity.reads
2003s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i2/0/44_633.trinity.reads
2003s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g2_i1/0/1_281.trinity.reads
2003s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g3_i1/0/1_491.trinity.reads
2003s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i3/0/1_8757.trinity.reads
2003s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i4/0/1_6795.trinity.reads
2004s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i5/0/1_8973.trinity.reads
2004s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN27_c0_g1_i1/0/1_261.trinity.reads
2004s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN4_c0_g1_i1/0/1_329.trinity.reads
2004s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN5_c0_g1_i1/0/1_252.trinity.reads
2004s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN7_c0_g1_i1/0/1_301.trinity.reads
2004s CMD: touch Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff.ok
2004s ##
2004s Done
2004s ##
2004s 
2004s Monday, November 4, 2024: 14:31:10	CMD: touch partitions.ok
2004s Monday, November 4, 2024: 14:31:10	CMD: find Dir_* -name '*reads' > read_files.list
2004s Monday, November 4, 2024: 14:31:10	CMD: touch read_files.list.ok
2004s Monday, November 4, 2024: 14:31:10	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
2004s Monday, November 4, 2024: 14:31:10	CMD: touch trinity_GG.cmds.ok
2004s Monday, November 4, 2024: 14:31:10	CMD: touch trinity_GG.cmds.ok
2004s 
2004s 
2004s --------------------------------------------------------------------------------
2004s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
2004s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
2004s --------------------------------------------------------------------------------
2004s 
2004s Monday, November 4, 2024: 14:31:10	CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -v -shuffle 
2004s Number of Commands: 85
2227s 
succeeded(1)   1.17647% completed.    
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succeeded(83)   97.6471% completed.    
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succeeded(85)   100% completed.    
2227s 
2227s All commands completed successfully. :-)
2227s 
2227s Monday, November 4, 2024: 14:34:53	CMD: find Dir_*  -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta.tmp
2227s Monday, November 4, 2024: 14:34:53	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta.gene_trans_map
2227s 
2227s 
2227s Finished. See /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta for reconstructed transcripts
2227s 
2227s 
2227s 
2227s outfile="test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta"
2227s asmsize=$(wc -c <"${outfile}")
2227s ok
2227s ./run_chr17_GG_wLongreads.sh
2227s if [ $asmsize -le 650000 ]; then
2227s     echo "Error, ${outfile} potentially incomplete"
2227s     exit 1
2227s else
2227s     echo "ok"
2227s     exit 0
2227s fi
2227s #!/bin/bash -ve
2227s 
2227s 
2227s $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
2227s 
2227s 
2227s      ______  ____   ____  ____   ____  ______  __ __
2227s     |      ||    \ |    ||    \ |    ||      ||  |  |
2227s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
2227s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
2227s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
2227s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
2227s       |__|  |__|\_||____||__|__||____|  |__|  |____/
2227s 
2227s     Trinity-v2.15.1
2227s 
2227s 
2227s 
2227s Monday, November 4, 2024: 14:34:53	CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl chr17.illumina.bam
2227s -appears to be a coordinate sorted bam file. ok.
2227s Monday, November 4, 2024: 14:34:53	CMD: mkdir -p /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir
2227s 
2227s 
2227s ----------------------------------------------------------------------------------
2227s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
2227s ----------------------------------------------------------------------------------
2227s 
2227s -found paired-end aligned read. Running in paired-end mode.
2227s Monday, November 4, 2024: 14:34:53	CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.illumina.bam
2228s Done with chr chr1.
2228s Monday, November 4, 2024: 14:34:54	CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.illumina.bam.norm_200.bam.ok
2228s * [Mon Nov  4 14:34:54 2024] Running CMD: java -jar /usr/share/java/picard.jar AddOrReplaceReadGroups I=/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam  O=/tmp/autopkgtest.vWCmNc/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
2229s INFO	2024-11-04 14:34:55	AddOrReplaceReadGroups	
2229s 
2229s ********** NOTE: Picard's command line syntax is changing.
2229s **********
2229s ********** For more information, please see:
2229s ********** 
2229s https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
2229s **********
2229s ********** The command line looks like this in the new syntax:
2229s **********
2229s **********    AddOrReplaceReadGroups -I /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam -O /tmp/autopkgtest.vWCmNc/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
2229s **********
2229s 
2229s 
2229s 14:34:55.501 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
2229s 14:34:55.503 WARN  NativeLibraryLoader - LD_LIBRARY_PATH = :/usr/lib/trinityrnaseq/trinity-plugins/htslib
2229s 14:34:55.504 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
2229s 14:34:55.506 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
2229s 14:34:55.506 WARN  NativeLibraryLoader - LD_LIBRARY_PATH = :/usr/lib/trinityrnaseq/trinity-plugins/htslib
2229s 14:34:55.506 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
2229s [Mon Nov 04 14:34:55 UTC 2024] AddOrReplaceReadGroups INPUT=/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam OUTPUT=/tmp/autopkgtest.vWCmNc/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
2229s [Mon Nov 04 14:34:55 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
2229s 14:34:55.521 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
2229s 14:34:55.527 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
2229s INFO	2024-11-04 14:34:55	AddOrReplaceReadGroups	Created read-group ID=PBLR PL=pacbio LB=lib2 SM=pacbio
2229s 
2229s 14:34:55.561 WARN  IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
2229s [Mon Nov 04 14:34:55 UTC 2024] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.00 minutes.
2229s Runtime.totalMemory()=67108864
2229s * [Mon Nov  4 14:34:55 2024] Running CMD: samtools merge /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.illumina.bam.norm_200.bam /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.pbio.bam.RGLR.bam && samtools index /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam
2230s Monday, November 4, 2024: 14:34:56	CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.vWCmNc/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 
2230s 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 
2230s -extracting read coordinates from merged_wRGLR.bam into merged_wRGLR.bam.read_coords
2230s 
2232s CMD: touch merged_wRGLR.bam.read_coords.ok
2232s 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
2232s CMD: cp /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam.read_coords /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam.read_coords.sort_by_readname
2233s CMD: /usr/bin/sort --parallel=5 -S2G -T . -k1,1 -k3,3n merged_wRGLR.bam.frag_coords > merged_wRGLR.bam.frag_coords.coord_sorted
2233s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl merged_wRGLR.bam.frag_coords > merged_wRGLR.bam.frag_coverage.wig
2250s 
[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
2250s CMD: /usr/lib/trinityrnaseq/util/support_scripts/define_coverage_partitions.pl merged_wRGLR.bam.frag_coverage.wig 1 + > merged_wRGLR.bam.minC1.gff
2254s CMD: touch merged_wRGLR.bam.minC1.gff.ok
2254s 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 
2254s // parsing paritions.
2254s 
[100]  
[116]  -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/60324_60754.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/60950_61267.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/61474_118580.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/205351_205672.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/210418_210982.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/213769_219690.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/229120_229684.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/263847_264260.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/270652_271297.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/281768_441038.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/441045_445940.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/511494_511801.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/512042_512389.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/512759_514091.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/514571_714865.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/714910_715353.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/715370_716236.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/716302_716978.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/717455_718543.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/718787_719490.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/719569_720181.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/720720_721596.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/721666_722031.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/726239_726536.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/729712_730684.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/730918_731668.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/731742_732126.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/732418_752287.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/752375_752769.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/753167_754706.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/758974_782331.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/782362_792510.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/793543_794109.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/795176_795754.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/799707_800316.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/800915_803792.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/981902_982655.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/997125_1091796.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1146722_1146846.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1148302_1149226.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1151011_1152011.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1153293_1153810.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1226770_1227467.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1257967_1400270.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1414443_1415081.trinity.reads
2254s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1420724_2022954.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2030147_2043980.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2044654_2045225.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2047917_2048512.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2049091_2049553.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2051694_2052378.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2053479_2053635.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2054237_2054372.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2054544_2056751.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2056812_2057391.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2058177_2058912.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2059847_2303836.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2303955_2336468.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2336627_2337019.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2337198_2381047.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2384152_2401123.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2401365_2401725.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2404365_2404707.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2405573_2732999.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2956146_2956563.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2975679_2985002.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2991366_3008124.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3020537_3033568.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3033777_3034364.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3035321_3035959.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3036150_3036658.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3267590_3274822.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3328495_3331689.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3421757_3422307.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3422776_3423370.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3440227_3513828.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3565576_3566168.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3566800_3572235.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3573782_3585901.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3586814_3587176.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3589817_3592166.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3592533_3592851.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3605115_3605237.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3606109_3607928.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3607968_3636272.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3636486_3668698.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3668798_3670060.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3670078_3670807.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3673537_3681945.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3689987_3695886.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3706252_3917856.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3923874_3964467.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3964821_3965192.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4001444_4001952.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4003050_4003706.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4004424_4555389.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4660854_4661151.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4667839_4668289.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4671192_4704136.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4704234_4705420.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4710502_4721496.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4731419_4733592.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4734646_4739376.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4787354_4789638.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4796155_4798495.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4805950_4806545.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4807192_4823373.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4833366_4897982.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4904417_4904897.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4927248_4928577.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4928729_4928949.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4929025_4934979.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4935086_4935300.trinity.reads
2255s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4935439_4945214.trinity.reads
2256s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4945652_4997520.trinity.reads
2256s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4997681_5001302.trinity.reads
2256s CMD: touch Dir_merged_wRGLR.bam.minC1.gff.ok
2256s ##
2256s Done
2256s ##
2256s 
2256s Monday, November 4, 2024: 14:35:22	CMD: touch partitions.ok
2256s Monday, November 4, 2024: 14:35:22	CMD: find Dir_* -name '*reads' > read_files.list
2256s Monday, November 4, 2024: 14:35:22	CMD: touch read_files.list.ok
2256s Monday, November 4, 2024: 14:35:22	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
2256s Monday, November 4, 2024: 14:35:22	CMD: touch trinity_GG.cmds.ok
2256s Monday, November 4, 2024: 14:35:22	CMD: touch trinity_GG.cmds.ok
2256s 
2256s 
2256s --------------------------------------------------------------------------------
2256s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
2256s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
2256s --------------------------------------------------------------------------------
2256s 
2256s Monday, November 4, 2024: 14:35:22	CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 5 -v -shuffle 
2256s Number of Commands: 44
3047s 
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.    
3047s 
3047s All commands completed successfully. :-)
3047s 
3047s Monday, November 4, 2024: 14:48:33	CMD: find Dir_*  -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta.tmp
3047s Monday, November 4, 2024: 14:48:33	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta.gene_trans_map
3047s 
3047s 
3047s Finished. See /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta for reconstructed transcripts
3047s 
3047s 
3047s find test_chr17_LR_GG_trinity_outdir/ -regex ".*allProbPaths.fasta" -exec cat {} \; | grep '>' | grep 'LR\$' > test_chr17_LR_GG_trinity_outdir.LR
3048s touch test
3048s make[1]: Leaving directory '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity'
3048s Running example in test_InSilicoReadNormalization...
3048s make[1]: Entering directory '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization'
3048s ./test_PE_normalization.sh
3048s -prepping seqs
3048s Converting input files. (both directions in parallel)
3048s if [[ $(wc -l <test_chr17_LR_GG_trinity_outdir.LR) -le 200 ]]; then
3048s     echo "Error, fewer than expected pbio read-integrated assembled transcripts"
3048s     exit 1
3048s fi
3048s 
3048s 
3048s exit 0
3048s #!/bin/bash -ve
3048s 
3048s CPU=$(nproc || sysctl -n hw.physicalcpu)
3048s 
3048s # just for testing purposes, use --max_cov 30 or higher for real applications.
3048s $TRINITY_HOME/util/insilico_read_normalization.pl --JM 2G --left ../test_DATA/reads.left.fq.gz --right ../test_DATA/reads.right.fq.gz --seqType fq --max_cov 5 --pairs_together --no_cleanup --CPU ${CPU} --tmp_dir_name tmp_PE_norm_dir --min_cov 2
3048s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz) >> left.fa
3048s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz) >> right.fa
3048s CMD finished (0 seconds)
3048s CMD finished (0 seconds)
3048s CMD: touch left.fa.ok
3048s CMD finished (0 seconds)
3048s CMD: touch right.fa.ok
3048s CMD finished (0 seconds)
3048s Done converting input files.CMD: cat left.fa right.fa > both.fa
3048s CMD finished (0 seconds)
3048s CMD: touch both.fa.ok
3048s CMD finished (0 seconds)
3048s -kmer counting.
3048s -------------------------------------------
3048s ----------- Jellyfish  --------------------
3048s -- (building a k-mer catalog from reads) --
3048s -------------------------------------------
3048s 
3048s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  both.fa
3049s CMD finished (1 seconds)
3049s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
3049s CMD finished (0 seconds)
3049s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
3049s CMD finished (0 seconds)
3049s CMD: touch jellyfish.K25.min2.kmers.fa.success
3049s CMD finished (0 seconds)
3049s -generating stats files
3049s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > left.fa.K25.stats
3049s -reading Kmer occurrences...
3049s 
3049s  done parsing 100964 Kmers, 100964 added, taking 0 seconds.
3050s STATS_GENERATION_TIME: 1 seconds.
3050s CMD finished (1 seconds)
3050s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > right.fa.K25.stats
3050s -reading Kmer occurrences...
3050s 
3050s  done parsing 100964 Kmers, 100964 added, taking 0 seconds.
3050s STATS_GENERATION_TIME: 0 seconds.
3050s CMD finished (0 seconds)
3050s CMD: touch left.fa.K25.stats.ok
3050s CMD finished (0 seconds)
3050s CMD: touch right.fa.K25.stats.ok
3050s CMD finished (0 seconds)
3050s -sorting each stats file by read name.
3050s 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
3050s CMD finished (0 seconds)
3050s 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
3050s CMD finished (0 seconds)
3050s CMD: touch left.fa.K25.stats.sort.ok
3050s CMD finished (0 seconds)
3050s CMD: touch right.fa.K25.stats.sort.ok
3050s CMD finished (0 seconds)
3050s -defining normalized reads
3050s 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
3050s -opening left.fa.K25.stats.sort
3050s -opening right.fa.K25.stats.sort
3050s -done opening files.
3050s CMD finished (0 seconds)
3050s CMD: touch pairs.K25.stats.ok
3050s CMD finished (0 seconds)
3050s 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
3051s 3826 / 30575 = 12.51% reads selected during normalization.
3051s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
3051s 1797 / 30575 = 5.88% reads discarded as below minimum coverage threshold=2
3051s CMD finished (1 seconds)
3051s CMD: touch pairs.K25.stats.C5.maxCV10000.accs.ok
3051s CMD finished (0 seconds)
3051s -search and capture.
3051s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz ... done prepping, now search and capture.
3051s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz
3051s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz ... done prepping, now search and capture.
3051s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz
3051s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.left.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq.ok
3051s CMD finished (0 seconds)
3051s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.right.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq.ok
3051s CMD finished (0 seconds)
3051s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.left.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq left.norm.fq
3051s CMD finished (0 seconds)
3051s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.right.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq right.norm.fq
3051s CMD finished (0 seconds)
3051s 
3051s 
3051s Normalization complete. See outputs: 
3051s 	/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.left.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq
3051s 	/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.right.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq
3051s 
3051s 
3051s 
3051s ./test_SE_normalization.sh
3051s #!/bin/bash -ve
3051s 
3051s if [ ! -e reads.single.fq ]; then
3051s     gunzip -c ../test_DATA/reads.left.fq.gz > reads.single.fq
3051s fi
3051s 
3051s 
3051s # just for testing purposes, use --max_cov 30 or higher for real applications.
3051s $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
3051s -prepping seqs
3051s CMD: seqtk-trinity seq -A -R 1  /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq >> single.fa
3051s CMD finished (0 seconds)
3051s CMD: touch single.fa.ok
3051s CMD finished (0 seconds)
3051s -kmer counting.
3051s -------------------------------------------
3051s ----------- Jellyfish  --------------------
3051s -- (building a k-mer catalog from reads) --
3051s -------------------------------------------
3051s 
3051s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  single.fa
3052s CMD finished (1 seconds)
3052s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
3052s CMD finished (0 seconds)
3052s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
3052s CMD finished (0 seconds)
3052s CMD: touch jellyfish.K25.min2.kmers.fa.success
3052s CMD finished (0 seconds)
3052s -generating stats files
3052s CMD: /usr/bin/fastaToKmerCoverageStats --reads single.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > single.fa.K25.stats
3052s -reading Kmer occurrences...
3052s 
3052s  done parsing 70076 Kmers, 70076 added, taking 0 seconds.
3053s STATS_GENERATION_TIME: 1 seconds.
3053s CMD finished (1 seconds)
3053s CMD: touch single.fa.K25.stats.ok
3053s CMD finished (0 seconds)
3053s -sorting each stats file by read name.
3053s 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
3053s CMD finished (0 seconds)
3053s CMD: touch single.fa.K25.stats.sort.ok
3053s CMD finished (0 seconds)
3053s -defining normalized reads
3053s 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
3053s 9127 / 30575 = 29.85% reads selected during normalization.
3053s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
3053s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=0
3053s CMD finished (0 seconds)
3053s CMD: touch single.fa.K25.stats.sort.maxC5.minC0.maxCV10000.accs.ok
3053s CMD finished (0 seconds)
3053s -search and capture.
3053s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq ... done prepping, now search and capture.
3053s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq
3053s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq.normalized_K25_maxC5_minC0_maxCV10000.fq.ok
3053s CMD finished (0 seconds)
3053s CMD: ln -sf /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq.normalized_K25_maxC5_minC0_maxCV10000.fq single.norm.fq
3053s CMD finished (0 seconds)
3053s 
3053s 
3053s Normalization complete. See outputs: 
3053s 	/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq.normalized_K25_maxC5_minC0_maxCV10000.fq
3053s 
3053s 
3053s 
3053s ./test_PE_normalization.mult_read_sets.sh
3053s #!/bin/bash -ve
3053s 
3053s CPU=$(nproc || sysctl -n hw.physicalcpu)
3053s 
3053s # just for testing purposes, use --max_cov 30 or higher for real applications.
3053s $TRINITY_HOME/util/insilico_read_normalization.pl --JM 2G \
3053s      --left ../test_DATA/reads.left.fq.gz,../test_DATA/reads2.left.fq.gz \
3053s      --right ../test_DATA/reads.right.fq.gz,../test_DATA/reads2.right.fq.gz \
3053s      --seqType fq --max_cov 5 --pairs_together --no_cleanup --CPU ${CPU} --tmp_dir_name tmp_PE_mult_norm_dir \
3053s      --output test_multi_read_sets_norm_outdir
3053s -prepping seqs
3053s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz) >> left.fa
3053s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz) >> right.fa
3053s CMD finished (0 seconds)
3053s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.left.fq.gz) >> left.fa
3053s CMD finished (0 seconds)
3053s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.right.fq.gz) >> right.fa
3053s CMD finished (0 seconds)
3053s CMD finished (0 seconds)
3053s CMD: touch left.fa.ok
3053s CMD finished (0 seconds)
3053s CMD: touch right.fa.ok
3053s CMD finished (0 seconds)
3053s Done converting input files.CMD: cat left.fa right.fa > both.fa
3053s CMD finished (0 seconds)
3053s CMD: touch both.fa.ok
3053s CMD finished (0 seconds)
3053s -kmer counting.
3053s -------------------------------------------
3053s ----------- Jellyfish  --------------------
3053s -- (building a k-mer catalog from reads) --
3053s -------------------------------------------
3053s 
3053s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  both.fa
3055s CMD finished (2 seconds)
3055s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
3055s CMD finished (0 seconds)
3055s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
3055s CMD finished (0 seconds)
3055s CMD: touch jellyfish.K25.min2.kmers.fa.success
3055s CMD finished (0 seconds)
3055s -generating stats files
3055s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > left.fa.K25.stats
3055s -reading Kmer occurrences...
3055s 
3055s  done parsing 518514 Kmers, 518514 added, taking 0 seconds.
3056s STATS_GENERATION_TIME: 1 seconds.
3056s CMD finished (1 seconds)
3056s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > right.fa.K25.stats
3056s -reading Kmer occurrences...
3056s 
3056s  done parsing 518514 Kmers, 518514 added, taking 0 seconds.
3057s STATS_GENERATION_TIME: 1 seconds.
3057s CMD finished (1 seconds)
3057s CMD: touch left.fa.K25.stats.ok
3057s CMD finished (0 seconds)
3057s CMD: touch right.fa.K25.stats.ok
3057s CMD finished (0 seconds)
3057s -sorting each stats file by read name.
3057s 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
3057s CMD finished (0 seconds)
3057s 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
3057s CMD finished (0 seconds)
3057s CMD: touch left.fa.K25.stats.sort.ok
3057s CMD finished (0 seconds)
3057s CMD: touch right.fa.K25.stats.sort.ok
3057s CMD finished (0 seconds)
3057s -defining normalized reads
3057s 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
3057s -opening left.fa.K25.stats.sort
3057s -opening right.fa.K25.stats.sort
3057s -done opening files.
3058s CMD finished (1 seconds)
3058s CMD: touch pairs.K25.stats.ok
3058s CMD finished (0 seconds)
3058s 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
3059s 7970 / 61150 = 13.03% reads selected during normalization.
3059s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles.
3059s 0 / 61150 = 0.00% reads discarded as below minimum coverage threshold=0
3059s CMD finished (1 seconds)
3059s CMD: touch pairs.K25.stats.C5.maxCV10000.accs.ok
3059s CMD finished (0 seconds)
3059s -search and capture.
3059s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.left.fq.gz ... done prepping, now search and capture.
3059s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz
3059s -preparing to extract selected reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.right.fq.gz ... done prepping, now search and capture.
3059s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz
3059s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.left.fq.gz
3059s -capturing normalized reads from: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.right.fq.gz
3059s CMD: touch /tmp/autopkgtest.vWCmNc/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
3059s CMD finished (0 seconds)
3059s CMD: touch /tmp/autopkgtest.vWCmNc/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
3059s CMD finished (0 seconds)
3059s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
3059s CMD finished (0 seconds)
3059s CMD: ln -sf /tmp/autopkgtest.vWCmNc/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
3059s CMD finished (0 seconds)
3059s 
3059s 
3059s Normalization complete. See outputs: 
3059s 	/tmp/autopkgtest.vWCmNc/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
3059s 	/tmp/autopkgtest.vWCmNc/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
3059s 
3059s 
3059s 
3059s touch test
3059s make[1]: Leaving directory '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization'
3059s Running example in test_DE_analysis...
3059s make[1]: Entering directory '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis'
3059s Running example in Candida_example...
3059s make[2]: Entering directory '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example'
3059s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_DE_analysis.pl  -m Trinity_trans.counts.matrix --method edgeR -s samples.txt -o edgeR_outdir
3059s Got 9 samples, and got: 10 data fields.
3059s 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
3059s Next: TR24|c0_g1_i1	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
3059s 
3059s $VAR1 = {
3059s           'wt_37_1' => 3,
3059s           'wt_ph8_3' => 7,
3059s           'wt_GSNO_3' => 4,
3059s           'wt_37_2' => 1,
3059s           'wt_37_3' => 2,
3059s           'wt_GSNO_2' => 6,
3059s           'wt_ph8_1' => 8,
3059s           'wt_GSNO_1' => 5,
3059s           'wt_ph8_2' => 9
3059s         };
3059s $VAR1 = {
3059s           'wt_ph8' => [
3059s                         'wt_ph8_1',
3059s                         'wt_ph8_2',
3059s                         'wt_ph8_3'
3059s                       ],
3059s           'wt_GSNO' => [
3059s                          'wt_GSNO_1',
3059s                          'wt_GSNO_2',
3059s                          'wt_GSNO_3'
3059s                        ],
3059s           'wt_37' => [
3059s                        'wt_37_1',
3059s                        'wt_37_2',
3059s                        'wt_37_3'
3059s                      ]
3059s         };
3059s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.wt_37.vs.wt_GSNO.EdgeR.Rscript
3059s Contrasts to perform are: $VAR1 = [
3059s           [
3059s             'wt_37',
3059s             'wt_GSNO'
3059s           ],
3059s           [
3059s             'wt_37',
3059s             'wt_ph8'
3059s           ],
3059s           [
3059s             'wt_GSNO',
3059s             'wt_ph8'
3059s           ]
3059s         ];
3060s Loading required package: edgeR
3060s Loading required package: limma
3060s Using classic mode.
3062s null device 
3062s           1 
3062s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.wt_37.vs.wt_ph8.EdgeR.Rscript
3062s Loading required package: edgeR
3062s Loading required package: limma
3062s Using classic mode.
3064s null device 
3064s           1 
3064s CMD: Rscript Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.wt_GSNO.vs.wt_ph8.EdgeR.Rscript
3064s Loading required package: edgeR
3064s Loading required package: limma
3065s Using classic mode.
3066s null device 
3066s           1 
3066s cd edgeR_outdir && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl  \
3066s --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt && \
3066s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt
3066s 
3066s 
3066s ** Found 2062 features as differentially expressed.
3066s 
3066s 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
3066s CMD: Rscript diffExpr.P0.001_C2.matrix.R
3067s Loading required package: BiocGenerics
3067s 
3067s Attaching package: ‘BiocGenerics’
3067s 
3067s The following objects are masked from ‘package:stats’:
3067s 
3067s     IQR, mad, sd, var, xtabs
3067s 
3067s The following objects are masked from ‘package:base’:
3067s 
3067s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3067s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3067s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3067s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3067s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3067s     tapply, union, unique, unsplit, which.max, which.min
3067s 
3067s Welcome to Bioconductor
3067s 
3067s     Vignettes contain introductory material; view with
3067s     'browseVignettes()'. To cite Bioconductor, see
3067s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3067s 
3068s [1] "Reading matrix file."
3068s 
3068s Attaching package: ‘fastcluster’
3068s 
3068s The following object is masked from ‘package:stats’:
3068s 
3068s     hclust
3068s 
3068s for plotting:: min.raw: -0.643115788375154 max.raw: 1
3068s null device 
3068s           1 
3069s for plotting:: min.raw: -7.50284849776958 max.raw: 7.50284849776958
3069s null device 
3069s           1 
3071s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_37-UP.subset 
3071s 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 
3071s 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 
3071s num discordant:  0 
3071s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_37-UP.subset) passes test.
3071s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset 
3071s 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 
3071s 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 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test.
3071s 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 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 
3071s num discordant:  0 
3071s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_37-UP.subset 
3071s 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 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 
3071s 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 22.72933File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_37-UP.subset) passes test.
3071s  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 
3071s num discordant:  0 
3071s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset 
3071s 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 
3071s 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 
3071s num discordant:  0 
3071s validating:  Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset 
3071s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
3071s 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 
3071s 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 File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test.
3071s 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 
3071s num discordant:  0 
3071s validating:  Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset 
3071s 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 56.147File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
3071s  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 
3071s 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 4004.8 953.5553 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 
3071s num discordant:  0 
3071s touch test_edgeR
3071s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_DE_analysis.pl  -m Trinity_trans.counts.matrix --method DESeq2 -s samples.txt -o DESeq2_outdir
3071s Got 9 samples, and got: 10 data fields.
3071s 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
3071s Next: TR24|c0_g1_i1	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
3071s 
3071s $VAR1 = {
3071s           'wt_ph8_3' => 7,
3071s           'wt_ph8_1' => 8,
3071s           'wt_ph8_2' => 9,
3071s           'wt_GSNO_1' => 5,
3071s           'wt_37_1' => 3,
3071s           'wt_GSNO_2' => 6,
3071s           'wt_37_3' => 2,
3071s           'wt_37_2' => 1,
3071s           'wt_GSNO_3' => 4
3071s         };
3071s $VAR1 = {
3071s           'wt_37' => [
3071s                        'wt_37_1',
3071s                        'wt_37_2',
3071s                        'wt_37_3'
3071s                      ],
3071s           'wt_ph8' => [
3071s                         'wt_ph8_1',
3071s                         'wt_ph8_2',
3071s                         'wt_ph8_3'
3071s                       ],
3071s           'wt_GSNO' => [
3071s                          'wt_GSNO_1',
3071s                          'wt_GSNO_2',
3071s                          'wt_GSNO_3'
3071s                        ]
3071s         };
3071s Contrasts to perform are: $VAR1 = [
3071s           [
3071s             'wt_37',
3071s             'wt_GSNO'
3071s           ],
3071s           [
3071s             'wt_37',
3071s             'wt_ph8'
3071s           ],
3071s           [
3071s             'wt_GSNO',
3071s             'wt_ph8'
3071s           ]
3071s         ];
3071s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.Rscript
3071s Loading required package: edgeR
3071s Loading required package: limma
3071s Loading required package: DESeq2
3071s Loading required package: S4Vectors
3071s Loading required package: stats4
3071s Loading required package: BiocGenerics
3071s 
3071s Attaching package: ‘BiocGenerics’
3071s 
3071s The following object is masked from ‘package:limma’:
3071s 
3071s     plotMA
3071s 
3071s The following objects are masked from ‘package:stats’:
3071s 
3071s     IQR, mad, sd, var, xtabs
3071s 
3071s The following objects are masked from ‘package:base’:
3071s 
3071s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3071s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3071s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3071s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3071s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3071s     tapply, union, unique, unsplit, which.max, which.min
3071s 
3072s 
3072s Attaching package: ‘S4Vectors’
3072s 
3072s The following object is masked from ‘package:utils’:
3072s 
3072s     findMatches
3072s 
3072s The following objects are masked from ‘package:base’:
3072s 
3072s     expand.grid, I, unname
3072s 
3072s Loading required package: IRanges
3073s Loading required package: GenomicRanges
3073s Loading required package: GenomeInfoDb
3073s Loading required package: SummarizedExperiment
3073s Loading required package: MatrixGenerics
3073s Loading required package: matrixStats
3073s 
3073s Attaching package: ‘MatrixGenerics’
3073s 
3073s The following objects are masked from ‘package:matrixStats’:
3073s 
3073s     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
3073s     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
3073s     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
3073s     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
3073s     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
3073s     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
3073s     colWeightedMeans, colWeightedMedians, colWeightedSds,
3073s     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
3073s     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
3073s     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
3073s     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
3073s     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
3073s     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
3073s     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
3073s     rowWeightedSds, rowWeightedVars
3073s 
3073s Loading required package: Biobase
3074s Welcome to Bioconductor
3074s 
3074s     Vignettes contain introductory material; view with
3074s     'browseVignettes()'. To cite Bioconductor, see
3074s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3074s 
3074s 
3074s Attaching package: ‘Biobase’
3074s 
3074s The following object is masked from ‘package:MatrixGenerics’:
3074s 
3074s     rowMedians
3074s 
3074s The following objects are masked from ‘package:matrixStats’:
3074s 
3074s     anyMissing, rowMedians
3074s 
3078s converting counts to integer mode
3078s estimating size factors
3078s estimating dispersions
3078s gene-wise dispersion estimates
3079s mean-dispersion relationship
3079s final dispersion estimates
3079s fitting model and testing
3082s null device 
3082s           1 
3082s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.Rscript
3082s Loading required package: edgeR
3082s Loading required package: limma
3082s Loading required package: DESeq2
3082s Loading required package: S4Vectors
3082s Loading required package: stats4
3082s Loading required package: BiocGenerics
3082s 
3082s Attaching package: ‘BiocGenerics’
3082s 
3082s The following object is masked from ‘package:limma’:
3082s 
3082s     plotMA
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 
3083s 
3083s Attaching package: ‘S4Vectors’
3083s 
3083s The following object is masked from ‘package:utils’:
3083s 
3083s     findMatches
3083s 
3083s The following objects are masked from ‘package:base’:
3083s 
3083s     expand.grid, I, unname
3083s 
3083s Loading required package: IRanges
3084s Loading required package: GenomicRanges
3084s Loading required package: GenomeInfoDb
3084s Loading required package: SummarizedExperiment
3084s Loading required package: MatrixGenerics
3084s Loading required package: matrixStats
3084s 
3084s Attaching package: ‘MatrixGenerics’
3084s 
3084s The following objects are masked from ‘package:matrixStats’:
3084s 
3084s     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
3084s     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
3084s     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
3084s     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
3084s     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
3084s     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
3084s     colWeightedMeans, colWeightedMedians, colWeightedSds,
3084s     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
3084s     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
3084s     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
3084s     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
3084s     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
3084s     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
3084s     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
3084s     rowWeightedSds, rowWeightedVars
3084s 
3084s Loading required package: Biobase
3085s Welcome to Bioconductor
3085s 
3085s     Vignettes contain introductory material; view with
3085s     'browseVignettes()'. To cite Bioconductor, see
3085s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3085s 
3085s 
3085s Attaching package: ‘Biobase’
3085s 
3085s The following object is masked from ‘package:MatrixGenerics’:
3085s 
3085s     rowMedians
3085s 
3085s The following objects are masked from ‘package:matrixStats’:
3085s 
3085s     anyMissing, rowMedians
3085s 
3089s converting counts to integer mode
3089s estimating size factors
3089s estimating dispersions
3089s gene-wise dispersion estimates
3090s mean-dispersion relationship
3090s final dispersion estimates
3090s fitting model and testing
3092s null device 
3092s           1 
3093s CMD: Rscript Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.Rscript
3093s Loading required package: edgeR
3093s Loading required package: limma
3093s Loading required package: DESeq2
3093s Loading required package: S4Vectors
3093s Loading required package: stats4
3093s Loading required package: BiocGenerics
3093s 
3093s Attaching package: ‘BiocGenerics’
3093s 
3093s The following object is masked from ‘package:limma’:
3093s 
3093s     plotMA
3093s 
3093s The following objects are masked from ‘package:stats’:
3093s 
3093s     IQR, mad, sd, var, xtabs
3093s 
3093s The following objects are masked from ‘package:base’:
3093s 
3093s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3093s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3093s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3093s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3093s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3093s     tapply, union, unique, unsplit, which.max, which.min
3093s 
3094s 
3094s Attaching package: ‘S4Vectors’
3094s 
3094s The following object is masked from ‘package:utils’:
3094s 
3094s     findMatches
3094s 
3094s The following objects are masked from ‘package:base’:
3094s 
3094s     expand.grid, I, unname
3094s 
3094s Loading required package: IRanges
3094s Loading required package: GenomicRanges
3094s Loading required package: GenomeInfoDb
3095s Loading required package: SummarizedExperiment
3095s Loading required package: MatrixGenerics
3095s Loading required package: matrixStats
3095s 
3095s Attaching package: ‘MatrixGenerics’
3095s 
3095s The following objects are masked from ‘package:matrixStats’:
3095s 
3095s     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
3095s     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
3095s     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
3095s     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
3095s     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
3095s     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
3095s     colWeightedMeans, colWeightedMedians, colWeightedSds,
3095s     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
3095s     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
3095s     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
3095s     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
3095s     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
3095s     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
3095s     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
3095s     rowWeightedSds, rowWeightedVars
3095s 
3095s Loading required package: Biobase
3096s Welcome to Bioconductor
3096s 
3096s     Vignettes contain introductory material; view with
3096s     'browseVignettes()'. To cite Bioconductor, see
3096s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3096s 
3096s 
3096s Attaching package: ‘Biobase’
3096s 
3096s The following object is masked from ‘package:MatrixGenerics’:
3096s 
3096s     rowMedians
3096s 
3096s The following objects are masked from ‘package:matrixStats’:
3096s 
3096s     anyMissing, rowMedians
3096s 
3099s converting counts to integer mode
3100s estimating size factors
3100s estimating dispersions
3100s gene-wise dispersion estimates
3100s mean-dispersion relationship
3100s final dispersion estimates
3101s fitting model and testing
3103s null device 
3103s           1 
3103s cd DESeq2_outdir && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl  \
3103s --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt --order_columns_by_samples_file && \
3103s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt
3103s 
3103s 
3103s ** Found 1783 features as differentially expressed.
3103s 
3103s 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 
3103s CMD: Rscript diffExpr.P0.001_C2.matrix.R
3103s Loading required package: BiocGenerics
3103s 
3103s Attaching package: ‘BiocGenerics’
3103s 
3103s The following objects are masked from ‘package:stats’:
3103s 
3103s     IQR, mad, sd, var, xtabs
3103s 
3103s The following objects are masked from ‘package:base’:
3103s 
3103s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3103s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3103s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3103s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3103s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3103s     tapply, union, unique, unsplit, which.max, which.min
3103s 
3104s Welcome to Bioconductor
3104s 
3104s     Vignettes contain introductory material; view with
3104s     'browseVignettes()'. To cite Bioconductor, see
3104s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3104s 
3104s 
3104s Attaching package: ‘fastcluster’
3104s 
3104s [1] "Reading matrix file."
3104s The following object is masked from ‘package:stats’:
3104s 
3104s     hclust
3104s 
3105s for plotting:: min.raw: -0.674993513119273 max.raw: 1
3105s Warning messages:
3105s 1: null device 
3105s           1 
3105s In heatmap.3(sample_cor_for_plot, dendrogram = "both", Rowv = RowV,  :
3105s   Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
3105s 2: In heatmap.3(sample_cor_for_plot, dendrogram = "both", Rowv = RowV,  :
3105s   Discrepancy: Colv is FALSE, while dendrogram is `none'. Omitting column dendogram.
3105s for plotting:: min.raw: -7.50284849776958 max.raw: 7.50284849776958
3106s null device 
3106s           1 
3106s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset 
3106s 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 
3106s 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 5.784 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 
3106s num discordant:  0 
3106s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset 
3106s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset) passes test.
3106s 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 
3106s 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 
3106s num discordant:  0 
3106s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset 
3106s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test.
3107s 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 
3107s 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 
3107s num discordant:  0 
3107s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset 
3107s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset) passes test.
3107s 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 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
3107s 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 
3107s 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 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 
3107s num discordant:  0 
3107s validating:  Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset 
3107s 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 
3107s 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 
3107s num discordant:  0 
3107s validating:  Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset 
3107s File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test.
3107s 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 
3107s 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 
3107s num discordant:  0 
3107s File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
3107s touch test_DESeq2
3107s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_DE_analysis.pl  -m Trinity_trans.counts.matrix --method voom -s samples.txt -o voom_outdir
3107s Got 9 samples, and got: 10 data fields.
3107s 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
3107s Next: TR24|c0_g1_i1	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
3107s 
3107s $VAR1 = {
3107s           'wt_GSNO_1' => 5,
3107s           'wt_ph8_3' => 7,
3107s           'wt_37_1' => 3,
3107s           'wt_37_2' => 1,
3107s           'wt_ph8_2' => 9,
3107s           'wt_GSNO_3' => 4,
3107s           'wt_ph8_1' => 8,
3107s           'wt_37_3' => 2,
3107s           'wt_GSNO_2' => 6
3107s         };
3107s $VAR1 = {
3107s           'wt_GSNO' => [
3107s                          'wt_GSNO_1',
3107s                          'wt_GSNO_2',
3107s                          'wt_GSNO_3'
3107s                        ],
3107s           'wt_ph8' => [
3107s                         'wt_ph8_1',
3107s                         'wt_ph8_2',
3107s                         'wt_ph8_3'
3107s                       ],
3107s           'wt_37' => [
3107s                        'wt_37_1',
3107s                        'wt_37_2',
3107s                        'wt_37_3'
3107s                      ]
3107s         };
3107s Contrasts to perform are: $VAR1 = [
3107s           [
3107s             'wt_37',
3107s             'wt_GSNO'
3107s           ],
3107s           [
3107s             'wt_37',
3107s             'wt_ph8'
3107s           ],
3107s           [
3107s             'wt_GSNO',
3107s             'wt_ph8'
3107s           ]
3107s         ];
3107s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.wt_37.vs.wt_GSNO.voom.Rscript
3107s Loading required package: limma
3108s null device 
3108s           1 
3108s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.wt_37.vs.wt_ph8.voom.Rscript
3108s Loading required package: limma
3110s null device 
3110s           1 
3110s CMD: Rscript Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.wt_GSNO.vs.wt_ph8.voom.Rscript
3110s Loading required package: limma
3112s null device 
3112s           1 
3112s cd voom_outdir && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl  \
3112s --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt && \
3112s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt
3112s 
3112s 
3112s ** Found 1817 features as differentially expressed.
3112s 
3112s 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
3112s CMD: Rscript diffExpr.P0.001_C2.matrix.R
3112s Loading required package: BiocGenerics
3112s 
3112s Attaching package: ‘BiocGenerics’
3112s 
3112s The following objects are masked from ‘package:stats’:
3112s 
3112s     IQR, mad, sd, var, xtabs
3112s 
3112s The following objects are masked from ‘package:base’:
3112s 
3112s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3112s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3112s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3112s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3112s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3112s     tapply, union, unique, unsplit, which.max, which.min
3112s 
3112s Welcome to Bioconductor
3112s 
3112s     Vignettes contain introductory material; view with
3112s     'browseVignettes()'. To cite Bioconductor, see
3112s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3112s 
3113s [1] "Reading matrix file."
3113s 
3113s Attaching package: ‘fastcluster’
3113s 
3113s The following object is masked from ‘package:stats’:
3113s 
3113s     hclust
3113s 
3113s for plotting:: min.raw: -0.680559894057534 max.raw: 1
3113s null device 
3113s           1 
3114s for plotting:: min.raw: -7.50284849776958 max.raw: 7.50284849776958
3114s null device 
3114s           1 
3115s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_37-UP.subset 
3115s sampleA_mean:  6030.232 20787.35 1833.283 1407.266 1046.9 4776.171 2191.464 4954.434 1371.045 1037.645 1013.064 1326.5 982.539 484.398 887.2083 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 
3115s 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 
3115s num discordant:  0 
3115s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_37-UP.subset) passes test.
3115s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset 
3115s 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 
3115s 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 106.9733File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test.
3115s  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 
3115s num discordant:  0 
3115s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_37-UP.subset 
3115s 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 1707.219 581.2863File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_37-UP.subset) passes test.
3115s  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 
3115s 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 
3115s num discordant:  0 
3115s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset 
3115s 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 
3115s 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 
3115s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
3115s num discordant:  0 
3115s validating:  Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset 
3115s sampleA_mean:  File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test.
3115s 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 
3115s 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 
3115s num discordant:  0 
3115s validating:  Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset 
3115s 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 
3115s 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 87.65567File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
3115s  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 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 
3115s num discordant:  0 
3115s touch test_voom
3115s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR -m Trinity_trans.TMM.EXPR.matrix -s samples.txt --heatmap --sample_cor_matrix --log2 --save
3115s CMD: Rscript Trinity_trans.TMM.EXPR.matrix.R
3116s Loading required package: BiocGenerics
3116s 
3116s Attaching package: ‘BiocGenerics’
3116s 
3116s The following objects are masked from ‘package:stats’:
3116s 
3116s     IQR, mad, sd, var, xtabs
3116s 
3116s The following objects are masked from ‘package:base’:
3116s 
3116s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3116s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3116s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3116s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3116s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3116s     tapply, union, unique, unsplit, which.max, which.min
3116s 
3116s Welcome to Bioconductor
3116s 
3116s     Vignettes contain introductory material; view with
3116s     'browseVignettes()'. To cite Bioconductor, see
3116s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3116s 
3117s 
3117s Attaching package: ‘fastcluster’
3117s 
3117s [1] "Reading matrix file."
3117s The following object is masked from ‘package:stats’:
3117s 
3117s     hclust
3117s 
3117s for plotting:: min.raw: 0.647032826340685 max.raw: 1
3117s null device 
3117s           1 
3122s for plotting:: min.raw: 0 max.raw: 15.3986319455363
3122s null device 
3122s           1 
3132s touch test_PtR_heatmap
3132s ./validate_results.pl
3132s DESeq2_outdir/diffExpr.P0.001_C2.matrix, count: 1784 DE features OK.
3132s edgeR_outdir/diffExpr.P0.001_C2.matrix, count: 2063 DE features OK.
3132s voom_outdir/diffExpr.P0.001_C2.matrix, count: 1818 DE features OK.
3132s make[2]: Leaving directory '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example'
3132s Running example in Spombe_example...
3132s make[2]: Entering directory '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example'
3132s /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
3132s Got 4 samples, and got: 5 data fields.
3132s Header: ds_rep1	hs_rep1	log_rep1	plat_rep1
3132s Next: TRINITY_DN5555_c0_g1	0.00	0.00	0.00	0.00
3132s 
3132s $VAR1 = {
3132s           'hs_rep1' => 2,
3132s           'ds_rep1' => 1,
3132s           'log_rep1' => 3,
3132s           'plat_rep1' => 4
3132s         };
3132s $VAR1 = {
3132s           'log_growth' => [
3132s                             'log_rep1'
3132s                           ],
3132s           'heatshock' => [
3132s                            'hs_rep1'
3132s                          ],
3132s           'plateau' => [
3132s                          'plat_rep1'
3132s                        ],
3132s           'diauxic_shift' => [
3132s                                'ds_rep1'
3132s                              ]
3132s         };
3132s Contrasts to perform are: $VAR1 = [
3132s           [
3132s             'diauxic_shift',
3132s             'heatshock'
3132s           ],
3132s           [
3132s             'diauxic_shift',
3132s             'log_growth'
3132s           ],
3132s           [
3132s             'diauxic_shift',
3132s             'plateau'
3132s           ],
3132s           [
3132s             'heatshock',
3132s             'log_growth'
3132s           ],
3132s           [
3132s             'heatshock',
3132s             'plateau'
3132s           ],
3132s           [
3132s             'log_growth',
3132s             'plateau'
3132s           ]
3132s         ];
3132s CMD: Rscript Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.diauxic_shift.vs.heatshock.EdgeR.Rscript
3133s Loading required package: edgeR
3133s Loading required package: limma
3133s null device 
3133s           1 
3133s CMD: Rscript Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.diauxic_shift.vs.log_growth.EdgeR.Rscript
3133s Loading required package: edgeR
3133s Loading required package: limma
3133s null device 
3133s           1 
3133s CMD: Rscript Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.diauxic_shift.vs.plateau.EdgeR.Rscript
3134s Loading required package: edgeR
3134s Loading required package: limma
3134s null device 
3134s           1 
3134s CMD: Rscript Trinity_genes.counts.matrix.heatshock_vs_log_growth.heatshock.vs.log_growth.EdgeR.Rscript
3134s Loading required package: edgeR
3134s Loading required package: limma
3135s null device 
3135s           1 
3135s CMD: Rscript Trinity_genes.counts.matrix.heatshock_vs_plateau.heatshock.vs.plateau.EdgeR.Rscript
3135s Loading required package: edgeR
3135s Loading required package: limma
3135s null device 
3135s           1 
3135s CMD: Rscript Trinity_genes.counts.matrix.log_growth_vs_plateau.log_growth.vs.plateau.EdgeR.Rscript
3135s Loading required package: edgeR
3135s Loading required package: limma
3136s null device 
3136s           1 
3136s cd edgeR_genes && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl -m ../Trinity_genes.TMM.EXPR.matrix \
3136s         -s ../samples.txt  --examine_GO_enrichment --GO_annots ../Trinotate_report.xls.gene_ontology --gene_lengths ../Trinity_genes.lengths && \
3136s            /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt
3136s 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 
3136s Loading required package: BiasedUrn
3136s Loading required package: geneLenDataBase
3146s 
3146s Loading required package: AnnotationDbi
3146s Loading required package: stats4
3146s Loading required package: BiocGenerics
3146s 
3146s Attaching package: ‘BiocGenerics’
3146s 
3146s The following objects are masked from ‘package:stats’:
3146s 
3146s     IQR, mad, sd, var, xtabs
3146s 
3146s The following objects are masked from ‘package:base’:
3146s 
3146s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3146s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3146s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3146s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3146s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3146s     tapply, union, unique, unsplit, which.max, which.min
3146s 
3146s Loading required package: Biobase
3146s Welcome to Bioconductor
3146s 
3146s     Vignettes contain introductory material; view with
3146s     'browseVignettes()'. To cite Bioconductor, see
3146s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3146s 
3146s Loading required package: IRanges
3146s Loading required package: S4Vectors
3146s 
3146s Attaching package: ‘S4Vectors’
3146s 
3146s The following object is masked from ‘package:geneLenDataBase’:
3146s 
3146s     unfactor
3146s 
3146s The following object is masked from ‘package:utils’:
3146s 
3146s     findMatches
3146s 
3146s The following objects are masked from ‘package:base’:
3146s 
3146s     expand.grid, I, unname
3146s 
3147s Processing category: custom_list
3147s Using manually entered categories.
3147s Calculating the p-values...
3148s 'select()' returned 1:1 mapping between keys and columns
3148s 
3148s 
3148s Done.
3148s 
3148s 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 
3148s Loading required package: BiasedUrn
3148s Loading required package: geneLenDataBase
3158s 
3158s Loading required package: AnnotationDbi
3158s Loading required package: stats4
3158s Loading required package: BiocGenerics
3158s 
3158s Attaching package: ‘BiocGenerics’
3158s 
3158s The following objects are masked from ‘package:stats’:
3158s 
3158s     IQR, mad, sd, var, xtabs
3158s 
3158s The following objects are masked from ‘package:base’:
3158s 
3158s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3158s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3158s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3158s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3158s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3158s     tapply, union, unique, unsplit, which.max, which.min
3158s 
3158s Loading required package: Biobase
3158s Welcome to Bioconductor
3158s 
3158s     Vignettes contain introductory material; view with
3158s     'browseVignettes()'. To cite Bioconductor, see
3158s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3158s 
3158s Loading required package: IRanges
3158s Loading required package: S4Vectors
3158s 
3158s Attaching package: ‘S4Vectors’
3158s 
3158s The following object is masked from ‘package:geneLenDataBase’:
3158s 
3158s     unfactor
3158s 
3158s The following object is masked from ‘package:utils’:
3158s 
3158s     findMatches
3158s 
3158s The following objects are masked from ‘package:base’:
3158s 
3158s     expand.grid, I, unname
3158s 
3159s Processing category: custom_list
3159s Using manually entered categories.
3159s Calculating the p-values...
3159s 'select()' returned 1:1 mapping between keys and columns
3160s 
3160s 
3160s Done.
3160s 
3160s 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 
3160s Loading required package: BiasedUrn
3160s Loading required package: geneLenDataBase
3169s 
3169s Loading required package: AnnotationDbi
3169s Loading required package: stats4
3169s Loading required package: BiocGenerics
3169s 
3169s Attaching package: ‘BiocGenerics’
3169s 
3169s The following objects are masked from ‘package:stats’:
3169s 
3169s     IQR, mad, sd, var, xtabs
3169s 
3169s The following objects are masked from ‘package:base’:
3169s 
3169s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3169s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3169s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3169s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3169s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3169s     tapply, union, unique, unsplit, which.max, which.min
3169s 
3169s Loading required package: Biobase
3169s Welcome to Bioconductor
3169s 
3169s     Vignettes contain introductory material; view with
3169s     'browseVignettes()'. To cite Bioconductor, see
3169s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3169s 
3169s Loading required package: IRanges
3169s Loading required package: S4Vectors
3169s 
3169s Attaching package: ‘S4Vectors’
3169s 
3169s The following object is masked from ‘package:geneLenDataBase’:
3169s 
3169s     unfactor
3169s 
3169s The following object is masked from ‘package:utils’:
3169s 
3169s     findMatches
3169s 
3169s The following objects are masked from ‘package:base’:
3169s 
3169s     expand.grid, I, unname
3169s 
3170s Processing category: custom_list
3170s Using manually entered categories.
3171s Calculating the p-values...
3171s 'select()' returned 1:1 mapping between keys and columns
3171s 
3171s 
3171s Done.
3171s 
3171s 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 
3172s Loading required package: BiasedUrn
3172s Loading required package: geneLenDataBase
3181s 
3181s Loading required package: AnnotationDbi
3181s Loading required package: stats4
3181s Loading required package: BiocGenerics
3181s 
3181s Attaching package: ‘BiocGenerics’
3181s 
3181s The following objects are masked from ‘package:stats’:
3181s 
3181s     IQR, mad, sd, var, xtabs
3181s 
3181s The following objects are masked from ‘package:base’:
3181s 
3181s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3181s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3181s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3181s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3181s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3181s     tapply, union, unique, unsplit, which.max, which.min
3181s 
3181s Loading required package: Biobase
3181s Welcome to Bioconductor
3181s 
3181s     Vignettes contain introductory material; view with
3181s     'browseVignettes()'. To cite Bioconductor, see
3181s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3181s 
3181s Loading required package: IRanges
3181s Loading required package: S4Vectors
3181s 
3181s Attaching package: ‘S4Vectors’
3181s 
3181s The following object is masked from ‘package:geneLenDataBase’:
3181s 
3181s     unfactor
3181s 
3181s The following object is masked from ‘package:utils’:
3181s 
3181s     findMatches
3181s 
3181s The following objects are masked from ‘package:base’:
3181s 
3181s     expand.grid, I, unname
3181s 
3182s Processing category: custom_list
3182s Using manually entered categories.
3183s Calculating the p-values...
3183s 'select()' returned 1:1 mapping between keys and columns
3183s 
3183s 
3183s Done.
3183s 
3183s 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 
3183s Loading required package: BiasedUrn
3183s Loading required package: geneLenDataBase
3192s 
3192s Loading required package: AnnotationDbi
3192s Loading required package: stats4
3192s Loading required package: BiocGenerics
3192s 
3192s Attaching package: ‘BiocGenerics’
3192s 
3192s The following objects are masked from ‘package:stats’:
3192s 
3192s     IQR, mad, sd, var, xtabs
3192s 
3192s The following objects are masked from ‘package:base’:
3192s 
3192s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3192s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3192s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3192s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3192s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3192s     tapply, union, unique, unsplit, which.max, which.min
3192s 
3192s Loading required package: Biobase
3192s Welcome to Bioconductor
3192s 
3192s     Vignettes contain introductory material; view with
3192s     'browseVignettes()'. To cite Bioconductor, see
3192s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3192s 
3192s Loading required package: IRanges
3192s Loading required package: S4Vectors
3192s 
3192s Attaching package: ‘S4Vectors’
3192s 
3192s The following object is masked from ‘package:geneLenDataBase’:
3192s 
3192s     unfactor
3192s 
3192s The following object is masked from ‘package:utils’:
3192s 
3192s     findMatches
3192s 
3192s The following objects are masked from ‘package:base’:
3192s 
3192s     expand.grid, I, unname
3192s 
3196s Warning message:
3196s In pcls(G) : initial point very close to some inequality constraints
3196s Processing category: custom_list
3196s Using manually entered categories.
3196s Calculating the p-values...
3197s 'select()' returned 1:1 mapping between keys and columns
3197s 
3197s 
3197s Done.
3197s 
3197s 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 
3197s Loading required package: BiasedUrn
3197s Loading required package: geneLenDataBase
3207s 
3207s Loading required package: AnnotationDbi
3207s Loading required package: stats4
3207s Loading required package: BiocGenerics
3207s 
3207s Attaching package: ‘BiocGenerics’
3207s 
3207s The following objects are masked from ‘package:stats’:
3207s 
3207s     IQR, mad, sd, var, xtabs
3207s 
3207s The following objects are masked from ‘package:base’:
3207s 
3207s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3207s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3207s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3207s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3207s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3207s     tapply, union, unique, unsplit, which.max, which.min
3207s 
3207s Loading required package: Biobase
3207s Welcome to Bioconductor
3207s 
3207s     Vignettes contain introductory material; view with
3207s     'browseVignettes()'. To cite Bioconductor, see
3207s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3207s 
3207s Loading required package: IRanges
3207s Loading required package: S4Vectors
3207s 
3207s Attaching package: ‘S4Vectors’
3207s 
3207s The following object is masked from ‘package:geneLenDataBase’:
3207s 
3207s     unfactor
3207s 
3207s The following object is masked from ‘package:utils’:
3207s 
3207s     findMatches
3207s 
3207s The following objects are masked from ‘package:base’:
3207s 
3207s     expand.grid, I, unname
3207s 
3210s Processing category: custom_list
3210s Using manually entered categories.
3211s Calculating the p-values...
3211s 'select()' returned 1:1 mapping between keys and columns
3211s 
3211s 
3211s Done.
3211s 
3211s 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 
3212s Loading required package: BiasedUrn
3212s Loading required package: geneLenDataBase
3221s 
3221s Loading required package: AnnotationDbi
3221s Loading required package: stats4
3221s Loading required package: BiocGenerics
3221s 
3221s Attaching package: ‘BiocGenerics’
3221s 
3221s The following objects are masked from ‘package:stats’:
3221s 
3221s     IQR, mad, sd, var, xtabs
3221s 
3221s The following objects are masked from ‘package:base’:
3221s 
3221s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3221s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3221s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3221s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3221s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3221s     tapply, union, unique, unsplit, which.max, which.min
3221s 
3221s Loading required package: Biobase
3221s Welcome to Bioconductor
3221s 
3221s     Vignettes contain introductory material; view with
3221s     'browseVignettes()'. To cite Bioconductor, see
3221s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3221s 
3221s Loading required package: IRanges
3221s Loading required package: S4Vectors
3221s 
3221s Attaching package: ‘S4Vectors’
3221s 
3221s The following object is masked from ‘package:geneLenDataBase’:
3221s 
3221s     unfactor
3221s 
3221s The following object is masked from ‘package:utils’:
3221s 
3221s     findMatches
3221s 
3221s The following objects are masked from ‘package:base’:
3221s 
3221s     expand.grid, I, unname
3221s 
3224s Warning message:
3224s In pcls(G) : initial point very close to some inequality constraints
3224s Processing category: custom_list
3224s Using manually entered categories.
3225s Calculating the p-values...
3225s 'select()' returned 1:1 mapping between keys and columns
3226s 
3226s 
3226s Done.
3226s 
3226s 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 
3226s Loading required package: BiasedUrn
3226s Loading required package: geneLenDataBase
3235s 
3235s Loading required package: AnnotationDbi
3235s Loading required package: stats4
3235s Loading required package: BiocGenerics
3235s 
3235s Attaching package: ‘BiocGenerics’
3235s 
3235s The following objects are masked from ‘package:stats’:
3235s 
3235s     IQR, mad, sd, var, xtabs
3235s 
3235s The following objects are masked from ‘package:base’:
3235s 
3235s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3235s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3235s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3235s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3235s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3235s     tapply, union, unique, unsplit, which.max, which.min
3235s 
3235s Loading required package: Biobase
3235s Welcome to Bioconductor
3235s 
3235s     Vignettes contain introductory material; view with
3235s     'browseVignettes()'. To cite Bioconductor, see
3235s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3235s 
3235s Loading required package: IRanges
3235s Loading required package: S4Vectors
3235s 
3235s Attaching package: ‘S4Vectors’
3235s 
3235s The following object is masked from ‘package:geneLenDataBase’:
3235s 
3235s     unfactor
3235s 
3235s The following object is masked from ‘package:utils’:
3235s 
3235s     findMatches
3235s 
3235s The following objects are masked from ‘package:base’:
3235s 
3235s     expand.grid, I, unname
3235s 
3237s Warning message:
3237s In newton(lsp = lsp, X = G$X, y = G$y, Eb = G$Eb, UrS = G$UrS, L = G$L,  :
3237s   Iteration limit reached without full convergence - check carefully
3237s Processing category: custom_list
3237s Using manually entered categories.
3237s Calculating the p-values...
3238s 'select()' returned 1:1 mapping between keys and columns
3238s 
3238s 
3238s Done.
3238s 
3238s 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 
3238s Loading required package: BiasedUrn
3238s Loading required package: geneLenDataBase
3247s 
3247s Loading required package: AnnotationDbi
3247s Loading required package: stats4
3247s Loading required package: BiocGenerics
3247s 
3247s Attaching package: ‘BiocGenerics’
3247s 
3247s The following objects are masked from ‘package:stats’:
3247s 
3247s     IQR, mad, sd, var, xtabs
3247s 
3247s The following objects are masked from ‘package:base’:
3247s 
3247s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3247s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3247s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3247s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3247s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3247s     tapply, union, unique, unsplit, which.max, which.min
3247s 
3247s Loading required package: Biobase
3247s Welcome to Bioconductor
3247s 
3247s     Vignettes contain introductory material; view with
3247s     'browseVignettes()'. To cite Bioconductor, see
3247s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3247s 
3247s Loading required package: IRanges
3247s Loading required package: S4Vectors
3247s 
3247s Attaching package: ‘S4Vectors’
3247s 
3247s The following object is masked from ‘package:geneLenDataBase’:
3247s 
3247s     unfactor
3247s 
3247s The following object is masked from ‘package:utils’:
3247s 
3247s     findMatches
3247s 
3247s The following objects are masked from ‘package:base’:
3247s 
3247s     expand.grid, I, unname
3247s 
3249s Warning message:
3249s In newton(lsp = lsp, X = G$X, y = G$y, Eb = G$Eb, UrS = G$UrS, L = G$L,  :
3249s   Iteration limit reached without full convergence - check carefully
3249s Processing category: custom_list
3249s Using manually entered categories.
3249s Calculating the p-values...
3250s 'select()' returned 1:1 mapping between keys and columns
3250s 
3250s 
3250s Done.
3250s 
3250s 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 
3250s Loading required package: BiasedUrn
3250s Loading required package: geneLenDataBase
3259s 
3259s Loading required package: AnnotationDbi
3259s Loading required package: stats4
3259s Loading required package: BiocGenerics
3259s 
3259s Attaching package: ‘BiocGenerics’
3259s 
3259s The following objects are masked from ‘package:stats’:
3259s 
3259s     IQR, mad, sd, var, xtabs
3259s 
3259s The following objects are masked from ‘package:base’:
3259s 
3259s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3259s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3259s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3259s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3259s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3259s     tapply, union, unique, unsplit, which.max, which.min
3259s 
3259s Loading required package: Biobase
3259s Welcome to Bioconductor
3259s 
3259s     Vignettes contain introductory material; view with
3259s     'browseVignettes()'. To cite Bioconductor, see
3259s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3259s 
3259s Loading required package: IRanges
3259s Loading required package: S4Vectors
3259s 
3259s Attaching package: ‘S4Vectors’
3259s 
3259s The following object is masked from ‘package:geneLenDataBase’:
3259s 
3259s     unfactor
3259s 
3259s The following object is masked from ‘package:utils’:
3259s 
3259s     findMatches
3259s 
3259s The following objects are masked from ‘package:base’:
3259s 
3259s     expand.grid, I, unname
3259s 
3261s Processing category: custom_list
3261s Using manually entered categories.
3261s Calculating the p-values...
3261s 'select()' returned 1:1 mapping between keys and columns
3261s 
3261s 
3261s Done.
3261s 
3261s 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 
3262s Loading required package: BiasedUrn
3262s Loading required package: geneLenDataBase
3271s 
3271s Loading required package: AnnotationDbi
3271s Loading required package: stats4
3271s Loading required package: BiocGenerics
3271s 
3271s Attaching package: ‘BiocGenerics’
3271s 
3271s The following objects are masked from ‘package:stats’:
3271s 
3271s     IQR, mad, sd, var, xtabs
3271s 
3271s The following objects are masked from ‘package:base’:
3271s 
3271s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3271s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3271s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3271s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3271s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3271s     tapply, union, unique, unsplit, which.max, which.min
3271s 
3271s Loading required package: Biobase
3271s Welcome to Bioconductor
3271s 
3271s     Vignettes contain introductory material; view with
3271s     'browseVignettes()'. To cite Bioconductor, see
3271s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3271s 
3271s Loading required package: IRanges
3271s Loading required package: S4Vectors
3271s 
3271s Attaching package: ‘S4Vectors’
3271s 
3271s The following object is masked from ‘package:geneLenDataBase’:
3271s 
3271s     unfactor
3271s 
3271s The following object is masked from ‘package:utils’:
3271s 
3271s     findMatches
3271s 
3271s The following objects are masked from ‘package:base’:
3271s 
3271s     expand.grid, I, unname
3271s 
3273s Processing category: custom_list
3273s Using manually entered categories.
3273s Calculating the p-values...
3273s 'select()' returned 1:1 mapping between keys and columns
3273s 
3273s 
3273s Done.
3273s 
3273s 
3273s 
3273s ** Found 25 features as differentially expressed.
3273s 
3273s 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
3273s CMD: Rscript diffExpr.P0.001_C2.matrix.R
3273s Loading required package: BiocGenerics
3274s 
3274s Attaching package: ‘BiocGenerics’
3274s 
3274s The following objects are masked from ‘package:stats’:
3274s 
3274s     IQR, mad, sd, var, xtabs
3274s 
3274s The following objects are masked from ‘package:base’:
3274s 
3274s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3274s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3274s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3274s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3274s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3274s     tapply, union, unique, unsplit, which.max, which.min
3274s 
3274s Welcome to Bioconductor
3274s 
3274s     Vignettes contain introductory material; view with
3274s     'browseVignettes()'. To cite Bioconductor, see
3274s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3274s 
3274s 
3274s Attaching package: ‘fastcluster’
3274s 
3274s The following object is masked from ‘package:stats’:
3274s 
3274s     hclust
3274s 
3274s [1] "Reading matrix file."
3275s for plotting:: min.raw: -0.790731955608766 max.raw: 1
3275s null device 
3275s           1 
3275s for plotting:: min.raw: -9.76652141391246 max.raw: 9.76652141391246
3275s null device 
3275s           1 
3275s validating:  Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset 
3275s no DE entries reported here.
3275s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset) passes test.
3275s validating:  Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.heatshock-UP.subset 
3275s sampleA_mean:  351.239 
3275s sampleB_mean:  10243.92 
3275s num discordant:  0 
3275s validating:  Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset 
3275s validating:  Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset 
3275s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.heatshock-UP.subset) passes test.
3275s no DE entries reported here.
3275s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset) passes test.
3275s no DE entries reported here.
3275s validating:  Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset 
3275s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset) passes test.
3275s sampleA_mean:  24474.99 
3275s sampleB_mean:  655.981 
3275s num discordant:  0 
3275s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset) passes test.
3275s validating:  Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset 
3275s no DE entries reported here.
3275s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset) passes test.
3275s validating:  Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.heatshock-UP.subset 
3275s 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 
3275s 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 
3275s num discordant:  0 
3275s validating:  Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset 
3275s File: (Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.heatshock-UP.subset) passes test.
3275s sampleA_mean:  2036.649 135.207 
3275s sampleB_mean:  11080.21 1620.935 
3275s num discordant:  0 
3275s validating:  Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.heatshock-UP.subset 
3275s File: (Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset) passes test.
3275s File: (Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.heatshock-UP.subset) passes test.
3275s no DE entries reported here.
3275s File: (Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset) passes test.
3275s File: (Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.log_growth-UP.subset) passes test.
3275s sampleA_mean:  7754.294 
3275s sampleB_mean:  252.38 
3275s num discordant:  0 
3275s validating:  Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset 
3275s validating:  Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.log_growth-UP.subset 
3275s sampleA_mean:  9466.084 
3275s sampleB_mean:  470.915 
3275s num discordant:  0 
3275s validating:  Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset 
3275s no DE entries reported here.
3275s File: (Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset) passes test.
3275s ./validate_results.pl 
3275s edgeR_genes/diffExpr.P0.001_C2.matrix, count: 26 DE features OK.
3275s 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.
3275s 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.
3275s touch test
3275s make[2]: Leaving directory '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example'
3275s make[1]: Leaving directory '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis'
3275s Running example in test_align_and_estimate_abundance...
3275s make[1]: Entering directory '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance'
3275s Running example in PAIRED_END_ABUNDANCE_ESTIMATION...
3275s make[2]: Entering directory '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION'
3275s ../align_and_estimate_tester.pl RSEM "samples.txt" "../../test_DATA/Trinity.fasta"
3275s CMD: ln -sf ../../test_DATA/Trinity.fasta .
3275s CMD: /usr/lib/trinityrnaseq/util/align_and_estimate_abundance.pl --transcripts Trinity.fasta --prep_reference  --left /tmp/autopkgtest.vWCmNc/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.vWCmNc/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 
3275s CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta > /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.gene_trans_map
3275s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.started
3275s CMD: bowtie2-build /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2
3275s Settings:
3275s   Output files: "/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.*.bt2"
3275s   Line rate: 6 (line is 64 bytes)
3275s   Lines per side: 1 (side is 64 bytes)
3275s   Offset rate: 4 (one in 16)
3275s   FTable chars: 10
3275s   Strings: unpacked
3275s   Max bucket size: default
3275s   Max bucket size, sqrt multiplier: default
3275s   Max bucket size, len divisor: 4
3275s   Difference-cover sample period: 1024
3275s   Endianness: little
3275s   Actual local endianness: little
3275s   Sanity checking: disabled
3275s   Assertions: disabled
3275s   Random seed: 0
3275s   Sizeofs: void*:8, int:4, long:8, size_t:8
3275s Input files DNA, FASTA:
3275s   /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta
3275s Reading reference sizes
3275s Building a SMALL index
3275s   Time reading reference sizes: 00:00:00
3275s Calculating joined length
3275s Writing header
3275s Reserving space for joined string
3275s Joining reference sequences
3275s   Time to join reference sequences: 00:00:00
3275s bmax according to bmaxDivN setting: 54360
3275s Using parameters --bmax 40770 --dcv 1024
3275s   Doing ahead-of-time memory usage test
3275s   Passed!  Constructing with these parameters: --bmax 40770 --dcv 1024
3275s Constructing suffix-array element generator
3275s Building DifferenceCoverSample
3275s   Building sPrime
3275s   Building sPrimeOrder
3275s   V-Sorting samples
3275s   V-Sorting samples time: 00:00:00
3275s   Allocating rank array
3275s   Ranking v-sort output
3275s   Ranking v-sort output time: 00:00:00
3275s   Invoking Larsson-Sadakane on ranks
3275s   Invoking Larsson-Sadakane on ranks time: 00:00:00
3275s   Sanity-checking and returning
3275s Building samples
3275s Reserving space for 12 sample suffixes
3275s Generating random suffixes
3275s QSorting 12 sample offsets, eliminating duplicates
3275s QSorting sample offsets, eliminating duplicates time: 00:00:00
3275s Multikey QSorting 12 samples
3275s   (Using difference cover)
3275s   Multikey QSorting samples time: 00:00:00
3275s Calculating bucket sizes
3275s Splitting and merging
3275s   Splitting and merging time: 00:00:00
3275s Split 2, merged 6; iterating...
3275s Splitting and merging
3275s   Splitting and merging time: 00:00:00
3275s Split 1, merged 2; iterating...
3275s Splitting and merging
3275s   Splitting and merging time: 00:00:00
3275s Split 1, merged 0; iterating...
3275s Splitting and merging
3275s   Splitting and merging time: 00:00:00
3275s Avg bucket size: 27179.5 (target: 40769)
3275s Converting suffix-array elements to index image
3275s Allocating ftab, absorbFtab
3275s Entering Ebwt loop
3275s Getting block 1 of 8
3275s   Reserving size (40770) for bucket 1
3275s   Calculating Z arrays for bucket 1
3275s   Entering block accumulator loop for bucket 1:
3275s   bucket 1: 10%
3275s   bucket 1: 20%
3275s   bucket 1: 30%
3275s   bucket 1: 40%
3275s   bucket 1: 50%
3275s   bucket 1: 60%
3275s   bucket 1: 70%
3275s   bucket 1: 80%
3275s   bucket 1: 90%
3275s   bucket 1: 100%
3275s   Sorting block of length 34231 for bucket 1
3275s   (Using difference cover)
3275s   Sorting block time: 00:00:00
3275s Returning block of 34232 for bucket 1
3275s Getting block 2 of 8
3275s   Reserving size (40770) for bucket 2
3275s   Calculating Z arrays for bucket 2
3275s   Entering block accumulator loop for bucket 2:
3275s   bucket 2: 10%
3275s   bucket 2: 20%
3275s   bucket 2: 30%
3275s   bucket 2: 40%
3275s   bucket 2: 50%
3275s   bucket 2: 60%
3275s   bucket 2: 70%
3275s   bucket 2: 80%
3275s   bucket 2: 90%
3275s   bucket 2: 100%
3275s   Sorting block of length 39793 for bucket 2
3275s   (Using difference cover)
3275s   Sorting block time: 00:00:00
3275s Returning block of 39794 for bucket 2
3275s Getting block 3 of 8
3275s   Reserving size (40770) for bucket 3
3275s   Calculating Z arrays for bucket 3
3275s   Entering block accumulator loop for bucket 3:
3275s   bucket 3: 10%
3275s   bucket 3: 20%
3275s   bucket 3: 30%
3275s   bucket 3: 40%
3275s   bucket 3: 50%
3275s   bucket 3: 60%
3275s   bucket 3: 70%
3275s   bucket 3: 80%
3275s   bucket 3: 90%
3275s   bucket 3: 100%
3275s   Sorting block of length 9793 for bucket 3
3275s   (Using difference cover)
3275s   Sorting block time: 00:00:00
3275s Returning block of 9794 for bucket 3
3275s Getting block 4 of 8
3275s   Reserving size (40770) for bucket 4
3275s   Calculating Z arrays for bucket 4
3275s   Entering block accumulator loop for bucket 4:
3275s   bucket 4: 10%
3275s   bucket 4: 20%
3275s   bucket 4: 30%
3275s   bucket 4: 40%
3275s   bucket 4: 50%
3275s   bucket 4: 60%
3275s   bucket 4: 70%
3275s   bucket 4: 80%
3275s   bucket 4: 90%
3275s   bucket 4: 100%
3275s   Sorting block of length 31901 for bucket 4
3275s   (Using difference cover)
3275s   Sorting block time: 00:00:00
3275s Returning block of 31902 for bucket 4
3275s Getting block 5 of 8
3275s   Reserving size (40770) for bucket 5
3275s   Calculating Z arrays for bucket 5
3275s   Entering block accumulator loop for bucket 5:
3275s   bucket 5: 10%
3275s   bucket 5: 20%
3275s   bucket 5: 30%
3275s   bucket 5: 40%
3275s   bucket 5: 50%
3275s   bucket 5: 60%
3275s   bucket 5: 70%
3275s   bucket 5: 80%
3275s   bucket 5: 90%
3275s   bucket 5: 100%
3275s   Sorting block of length 10600 for bucket 5
3275s   (Using difference cover)
3275s   Sorting block time: 00:00:00
3275s Returning block of 10601 for bucket 5
3275s Getting block 6 of 8
3275s   Reserving size (40770) for bucket 6
3275s   Calculating Z arrays for bucket 6
3275s   Entering block accumulator loop for bucket 6:
3275s   bucket 6: 10%
3275s   bucket 6: 20%
3275s   bucket 6: 30%
3275s   bucket 6: 40%
3275s   bucket 6: 50%
3275s   bucket 6: 60%
3275s   bucket 6: 70%
3275s   bucket 6: 80%
3275s   bucket 6: 90%
3275s   bucket 6: 100%
3275s   Sorting block of length 40652 for bucket 6
3275s   (Using difference cover)
3275s   Sorting block time: 00:00:00
3275s Returning block of 40653 for bucket 6
3275s Getting block 7 of 8
3275s   Reserving size (40770) for bucket 7
3275s   Calculating Z arrays for bucket 7
3275s   Entering block accumulator loop for bucket 7:
3275s   bucket 7: 10%
3275s   bucket 7: 20%
3275s   bucket 7: 30%
3275s   bucket 7: 40%
3275s   bucket 7: 50%
3275s   bucket 7: 60%
3275s   bucket 7: 70%
3275s   bucket 7: 80%
3275s   bucket 7: 90%
3275s   bucket 7: 100%
3275s   Sorting block of length 18337 for bucket 7
3275s   (Using difference cover)
3275s   Sorting block time: 00:00:00
3275s Returning block of 18338 for bucket 7
3275s Getting block 8 of 8
3275s   Reserving size (40770) for bucket 8
3275s   Calculating Z arrays for bucket 8
3275s   Entering block accumulator loop for bucket 8:
3275s   bucket 8: 10%
3275s   bucket 8: 20%
3275s   bucket 8: 30%
3275s   bucket 8: 40%
3275s   bucket 8: 50%
3275s   bucket 8: 60%
3275s   bucket 8: 70%
3275s   bucket 8: 80%
3275s   bucket 8: 90%
3275s   bucket 8: 100%
3275s   Sorting block of length 32129 for bucket 8
3275s   (Using difference cover)
3275s   Sorting block time: 00:00:00
3275s Returning block of 32130 for bucket 8
3275s Exited Ebwt loop
3275s fchr[A]: 0
3275s fchr[C]: 59864
3275s fchr[G]: 108205
3275s fchr[T]: 157829
3275s fchr[$]: 217443
3275s Exiting Ebwt::buildToDisk()
3275s Returning from initFromVector
3275s Wrote 4313663 bytes to primary EBWT file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.1.bt2.tmp
3275s Wrote 54368 bytes to secondary EBWT file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.2.bt2.tmp
3275s Re-opening _in1 and _in2 as input streams
3275s Returning from Ebwt constructor
3275s Headers:
3275s     len: 217443
3275s     bwtLen: 217444
3275s     sz: 54361
3275s     bwtSz: 54361
3275s     lineRate: 6
3275s     offRate: 4
3275s     offMask: 0xfffffff0
3275s     ftabChars: 10
3275s     eftabLen: 20
3275s     eftabSz: 80
3275s     ftabLen: 1048577
3275s     ftabSz: 4194308
3275s     offsLen: 13591
3275s     offsSz: 54364
3275s     lineSz: 64
3275s     sideSz: 64
3275s     sideBwtSz: 48
3275s     sideBwtLen: 192
3275s     numSides: 1133
3275s     numLines: 1133
3275s     ebwtTotLen: 72512
3275s     ebwtTotSz: 72512
3275s     color: 0
3275s     reverse: 0
3275s Total time for call to driver() for forward index: 00:00:00
3275s Reading reference sizes
3275s   Time reading reference sizes: 00:00:00
3275s Calculating joined length
3275s Writing header
3275s Reserving space for joined string
3275s Joining reference sequences
3275s   Time to join reference sequences: 00:00:00
3275s   Time to reverse reference sequence: 00:00:00
3275s bmax according to bmaxDivN setting: 54360
3275s Using parameters --bmax 40770 --dcv 1024
3275s   Doing ahead-of-time memory usage test
3275s   Passed!  Constructing with these parameters: --bmax 40770 --dcv 1024
3275s Constructing suffix-array element generator
3275s Building DifferenceCoverSample
3275s   Building sPrime
3275s   Building sPrimeOrder
3275s   V-Sorting samples
3275s   V-Sorting samples time: 00:00:00
3275s   Allocating rank array
3275s   Ranking v-sort output
3275s   Ranking v-sort output time: 00:00:00
3275s   Invoking Larsson-Sadakane on ranks
3275s   Invoking Larsson-Sadakane on ranks time: 00:00:00
3275s   Sanity-checking and returning
3275s Building samples
3275s Reserving space for 12 sample suffixes
3275s Generating random suffixes
3275s QSorting 12 sample offsets, eliminating duplicates
3275s QSorting sample offsets, eliminating duplicates time: 00:00:00
3275s Multikey QSorting 12 samples
3275s   (Using difference cover)
3275s   Multikey QSorting samples time: 00:00:00
3275s Calculating bucket sizes
3275s Splitting and merging
3275s   Splitting and merging time: 00:00:00
3275s Split 1, merged 6; iterating...
3275s Splitting and merging
3275s   Splitting and merging time: 00:00:00
3275s Avg bucket size: 31062.4 (target: 40769)
3275s Converting suffix-array elements to index image
3275s Allocating ftab, absorbFtab
3275s Entering Ebwt loop
3275s Getting block 1 of 7
3275s   Reserving size (40770) for bucket 1
3275s   Calculating Z arrays for bucket 1
3275s   Entering block accumulator loop for bucket 1:
3275s   bucket 1: 10%
3275s   bucket 1: 20%
3275s   bucket 1: 30%
3275s   bucket 1: 40%
3275s   bucket 1: 50%
3275s   bucket 1: 60%
3275s   bucket 1: 70%
3275s   bucket 1: 80%
3275s   bucket 1: 90%
3275s   bucket 1: 100%
3275s   Sorting block of length 37058 for bucket 1
3275s   (Using difference cover)
3275s   Sorting block time: 00:00:00
3275s Returning block of 37059 for bucket 1
3275s Getting block 2 of 7
3275s   Reserving size (40770) for bucket 2
3275s   Calculating Z arrays for bucket 2
3275s   Entering block accumulator loop for bucket 2:
3275s   bucket 2: 10%
3275s   bucket 2: 20%
3275s   bucket 2: 30%
3275s   bucket 2: 40%
3275s   bucket 2: 50%
3275s   bucket 2: 60%
3275s   bucket 2: 70%
3275s   bucket 2: 80%
3275s   bucket 2: 90%
3275s   bucket 2: 100%
3275s   Sorting block of length 17846 for bucket 2
3275s   (Using difference cover)
3275s   Sorting block time: 00:00:00
3275s Returning block of 17847 for bucket 2
3275s Getting block 3 of 7
3275s   Reserving size (40770) for bucket 3
3275s   Calculating Z arrays for bucket 3
3275s   Entering block accumulator loop for bucket 3:
3275s   bucket 3: 10%
3275s   bucket 3: 20%
3275s   bucket 3: 30%
3275s   bucket 3: 40%
3275s   bucket 3: 50%
3275s   bucket 3: 60%
3275s   bucket 3: 70%
3275s   bucket 3: 80%
3275s   bucket 3: 90%
3275s   bucket 3: 100%
3275s   Sorting block of length 39327 for bucket 3
3275s   (Using difference cover)
3275s   Sorting block time: 00:00:00
3275s Returning block of 39328 for bucket 3
3275s Getting block 4 of 7
3275s   Reserving size (40770) for bucket 4
3275s   Calculating Z arrays for bucket 4
3275s   Entering block accumulator loop for bucket 4:
3275s   bucket 4: 10%
3275s   bucket 4: 20%
3275s   bucket 4: 30%
3275s   bucket 4: 40%
3275s   bucket 4: 50%
3275s   bucket 4: 60%
3275s   bucket 4: 70%
3275s   bucket 4: 80%
3275s   bucket 4: 90%
3275s   bucket 4: 100%
3275s   Sorting block of length 34139 for bucket 4
3275s   (Using difference cover)
3275s   Sorting block time: 00:00:00
3275s Returning block of 34140 for bucket 4
3275s Getting block 5 of 7
3275s   Reserving size (40770) for bucket 5
3275s   Calculating Z arrays for bucket 5
3275s   Entering block accumulator loop for bucket 5:
3275s   bucket 5: 10%
3275s   bucket 5: 20%
3275s   bucket 5: 30%
3275s   bucket 5: 40%
3275s   bucket 5: 50%
3275s   bucket 5: 60%
3275s   bucket 5: 70%
3275s   bucket 5: 80%
3275s   bucket 5: 90%
3275s   bucket 5: 100%
3275s   Sorting block of length 31038 for bucket 5
3275s   (Using difference cover)
3275s   Sorting block time: 00:00:00
3275s Returning block of 31039 for bucket 5
3275s Getting block 6 of 7
3275s   Reserving size (40770) for bucket 6
3275s   Calculating Z arrays for bucket 6
3275s   Entering block accumulator loop for bucket 6:
3275s   bucket 6: 10%
3275s   bucket 6: 20%
3275s   bucket 6: 30%
3275s   bucket 6: 40%
3275s   bucket 6: 50%
3275s   bucket 6: 60%
3275s   bucket 6: 70%
3275s   bucket 6: 80%
3275s   bucket 6: 90%
3275s   bucket 6: 100%
3275s   Sorting block of length 21215 for bucket 6
3275s   (Using difference cover)
3275s   Sorting block time: 00:00:00
3275s Returning block of 21216 for bucket 6
3275s Getting block 7 of 7
3275s   Reserving size (40770) for bucket 7
3275s   Calculating Z arrays for bucket 7
3275s   Entering block accumulator loop for bucket 7:
3275s   bucket 7: 10%
3275s   bucket 7: 20%
3275s   bucket 7: 30%
3275s   bucket 7: 40%
3275s   bucket 7: 50%
3275s   bucket 7: 60%
3275s   bucket 7: 70%
3275s   bucket 7: 80%
3275s   bucket 7: 90%
3275s   bucket 7: 100%
3275s   Sorting block of length 36814 for bucket 7
3275s   (Using difference cover)
3275s   Sorting block time: 00:00:00
3275s Returning block of 36815 for bucket 7
3275s Exited Ebwt loop
3275s fchr[A]: 0
3275s fchr[C]: 59864
3275s fchr[G]: 108205
3275s fchr[T]: 157829
3275s fchr[$]: 217443
3275s Exiting Ebwt::buildToDisk()
3275s Returning from initFromVector
3275s Wrote 4313663 bytes to primary EBWT file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.1.bt2.tmp
3275s Wrote 54368 bytes to secondary EBWT file: /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.2.bt2.tmp
3275s Re-opening _in1 and _in2 as input streams
3275s Returning from Ebwt constructor
3275s Headers:
3275s     len: 217443
3275s     bwtLen: 217444
3275s     sz: 54361
3275s     bwtSz: 54361
3275s     lineRate: 6
3275s     offRate: 4
3275s     offMask: 0xfffffff0
3275s     ftabChars: 10
3275s     eftabLen: 20
3275s     eftabSz: 80
3275s     ftabLen: 1048577
3275s     ftabSz: 4194308
3275s     offsLen: 13591
3275s     offsSz: 54364
3275s     lineSz: 64
3275s     sideSz: 64
3275s     sideBwtSz: 48
3275s     sideBwtLen: 192
3275s     numSides: 1133
3275s     numLines: 1133
3275s     ebwtTotLen: 72512
3275s     ebwtTotSz: 72512
3275s     color: 0
3275s     reverse: 1
3275s Total time for backward call to driver() for mirror index: 00:00:00
3275s Renaming /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.3.bt2
3275s Renaming /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.4.bt2
3275s Renaming /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.1.bt2
3275s Renaming /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.2.bt2
3275s Renaming /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.1.bt2
3275s Renaming /tmp/autopkgtest.vWCmNc/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.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.2.bt2
3275s CMD: touch /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.rsem.prepped.started
3275s CMD: rsem-prepare-reference  --transcript-to-gene-map /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.gene_trans_map /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM
3276s rsem-synthesis-reference-transcripts /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM 0 1 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.gene_trans_map /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta
3276s Transcript Information File is generated!
3276s Group File is generated!
3276s Extracted Sequences File is generated!
3276s 
3276s rsem-preref /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.transcripts.fa 1 /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM
3276s Refs.makeRefs finished!
3276s Refs.saveRefs finished!
3276s /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.idx.fa is generated!
3276s /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.n2g.idx.fa is generated!
3276s 
3276s $VAR1 = [
3276s           {
3276s             'output_dir' => 'RSEM-heatshock',
3276s             'left' => '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.left.fq.gz',
3276s             'right' => '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.right.fq.gz'
3276s           }
3276s         ];
3276s CMD: set -o pipefail && bowtie2 --no-mixed --no-discordant --gbar 1000 --end-to-end -k 200  -q -X 800 -x /tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2 -1 /tmp/autopkgtest.vWCmNc/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.vWCmNc/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 
3276s 10000 reads; of these:
3276s   10000 (100.00%) were paired; of these:
3276s     7088 (70.88%) aligned concordantly 0 times
3276s     1764 (17.64%) aligned concordantly exactly 1 time
3276s     1148 (11.48%) aligned concordantly >1 times
3276s 29.12% overall alignment rate
3276s [bam_sort_core] merging from 0 files and 4 in-memory blocks...
3276s CMD: touch bowtie2.bam.ok
3276s CMD: convert-sam-for-rsem -p 4 bowtie2.bam bowtie2.bam.for_rsem
3276s samtools sort -n -@ 4 -m 1G -o bowtie2.bam.for_rsem.tmp.bam bowtie2.bam
3276s "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!
3276s samtools sort: couldn't allocate memory for bam_mem
3276s 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.
3276s Error, cmd:
3276s /usr/lib/trinityrnaseq/util/align_and_estimate_abundance.pl --transcripts Trinity.fasta --prep_reference  --left /tmp/autopkgtest.vWCmNc/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.vWCmNc/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 
3276s  died with ret (512) at /usr/lib/trinityrnaseq/PerlLib/Process_cmd.pm line 19.
3276s 	Process_cmd::process_cmd("/usr/lib/trinityrnaseq/util/align_and_estimate_abundance.pl -"...) called at ../align_and_estimate_tester.pl line 98
3276s make[2]: Leaving directory '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION'
3276s make[2]: *** [Makefile:25: test_RSEM] Error 2
3276s make[1]: Leaving directory '/tmp/autopkgtest.vWCmNc/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance'
3276s make[1]: *** [Makefile:8: test] Error 2
3276s make: *** [Makefile:18: test] Error 2
3277s autopkgtest [14:52:23]: test run-tests: -----------------------]
3277s run-tests            FAIL non-zero exit status 2
3277s autopkgtest [14:52:23]: test run-tests:  - - - - - - - - - - results - - - - - - - - - -
3278s autopkgtest [14:52:24]: @@@@@@@@@@@@@@@@@@@@ summary
3278s run-tests            FAIL non-zero exit status 2
3289s nova [W] Skipping flock for amd64
3289s Creating nova instance adt-plucky-amd64-trinityrnaseq-20241104-124444-juju-7f2275-prod-proposed-migration-environment-2-8ddd7891-3aa5-4000-b615-0d9b2a85ced4 from image adt/ubuntu-plucky-amd64-server-20241104.img (UUID 0ab90577-a6b7-4a72-9ab8-957838d495c0)...