0s autopkgtest [10:08:35]: starting date and time: 2024-11-01 10:08:35+0000
  0s autopkgtest [10:08:35]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [10:08:35]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9qk9nuuh/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:liburi-perl --apt-upgrade trinityrnaseq --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=liburi-perl/5.30-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-48.secgroup --name adt-plucky-arm64-trinityrnaseq-20241101-100834-juju-7f2275-prod-proposed-migration-environment-2-1c5a00f7-79e8-47f1-8fcb-e9b5e3707bd8 --image adt/ubuntu-plucky-arm64-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/
107s autopkgtest [10:10:22]: testbed dpkg architecture: arm64
107s autopkgtest [10:10:22]: testbed apt version: 2.9.8
107s autopkgtest [10:10:22]: @@@@@@@@@@@@@@@@@@@@ test bed setup
108s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
108s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [194 kB]
109s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [3094 kB]
109s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
109s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [51.2 kB]
109s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [247 kB]
109s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB]
109s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [2058 kB]
110s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [39.5 kB]
110s Fetched 5816 kB in 2s (2896 kB/s)
110s Reading package lists...
113s Reading package lists...
114s Building dependency tree...
114s Reading state information...
114s Calculating upgrade...
115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
115s Reading package lists...
115s Building dependency tree...
115s Reading state information...
116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
116s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
116s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
116s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
116s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
117s Reading package lists...
117s Reading package lists...
118s Building dependency tree...
118s Reading state information...
118s Calculating upgrade...
119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
119s Reading package lists...
119s Building dependency tree...
119s Reading state information...
120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
123s autopkgtest [10:10:38]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024
123s autopkgtest [10:10:38]: @@@@@@@@@@@@@@@@@@@@ apt-source trinityrnaseq
141s Get:1 http://ftpmaster.internal/ubuntu plucky/universe trinityrnaseq 2.15.1+dfsg-5build1 (dsc) [2629 B]
141s Get:2 http://ftpmaster.internal/ubuntu plucky/universe trinityrnaseq 2.15.1+dfsg-5build1 (tar) [307 MB]
141s Get:3 http://ftpmaster.internal/ubuntu plucky/universe trinityrnaseq 2.15.1+dfsg-5build1 (diff) [39.4 kB]
141s gpgv: Signature made Sun Apr 14 18:57:26 2024 UTC
141s gpgv:                using RSA key AC0A4FF12611B6FCCF01C111393587D97D86500B
141s gpgv: Can't check signature: No public key
141s dpkg-source: warning: cannot verify inline signature for ./trinityrnaseq_2.15.1+dfsg-5build1.dsc: no acceptable signature found
148s autopkgtest [10:11:03]: testing package trinityrnaseq version 2.15.1+dfsg-5build1
149s autopkgtest [10:11:04]: build not needed
173s autopkgtest [10:11:28]: test run-tests: preparing testbed
174s Reading package lists...
175s Building dependency tree...
175s Reading state information...
175s Starting pkgProblemResolver with broken count: 0
175s Starting 2 pkgProblemResolver with broken count: 0
175s Done
176s The following additional packages will be installed:
176s   adwaita-icon-theme at-spi2-common berkeley-express bowtie bowtie2
176s   ca-certificates-java dconf-gsettings-backend dconf-service default-jre
176s   default-jre-headless fontconfig fontconfig-config fonts-dejavu-core
176s   fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings
176s   fonts-lmodern fonts-mathjax gtk-update-icon-cache hicolor-icon-theme hisat2
176s   humanity-icon-theme jaligner java-common javascript-common jellyfish
176s   kallisto libapache-pom-java libasan8 libasound2-data libasound2t64
176s   libatinject-jsr330-api-java libatk-bridge2.0-0t64 libatk1.0-0t64
176s   libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3
176s   libbamtools2.5.2 libbarclay-java libbibtex-parser-perl libblas3 libboost-dev
176s   libboost-filesystem1.83.0 libboost-iostreams1.83.0
176s   libboost-program-options1.83.0 libboost-thread1.83.0 libboost1.83-dev
176s   libcairo-gobject2 libcairo2 libclone-perl libcolord2 libcommons-codec-java
176s   libcommons-compress-java libcommons-io-java libcommons-jexl2-java
176s   libcommons-lang3-java libcommons-logging-java libcommons-math3-java
176s   libcommons-parent-java libcups2t64 libdatrie1 libdconf1 libdeflate0
176s   libdrm-amdgpu1 libdrm-radeon1 libencode-locale-perl libepoxy0
176s   liberror-prone-java libfile-listing-perl libfontconfig1 libfreemarker-java
176s   libgatk-native-bindings-java libgbm1 libgcc-14-dev libgdk-pixbuf-2.0-0
176s   libgdk-pixbuf2.0-common libgetopt-java libgfortran5 libgif7 libgkl-java
176s   libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1
176s   libgoogle-gson-java libgraphite2-3 libgtk-3-0t64 libgtk-3-common
176s   libguava-java libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl
176s   libhtml-tree-perl libhts3t64 libhtscodecs2 libhtsjdk-java
176s   libhttp-cookies-perl libhttp-date-perl libhttp-message-perl
176s   libhttp-negotiate-perl libhttpclient-java libhttpcore-java libhwasan0
176s   libhwloc15 libice6 libio-html-perl libio-socket-ssl-perl libio-string-perl
176s   libitm1 libjbig0 libjbzip2-java libjellyfish-2.0-2 libjemalloc2
176s   libjoptsimple-java libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootstrap4
176s   libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery
176s   libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json
176s   libjs-lunr libjs-mathjax libjs-microplugin.js libjs-modernizr
176s   libjs-popper.js libjs-prettify libjs-sifter.js libjs-sphinxdoc
176s   libjs-twitter-bootstrap-datepicker libjs-underscore libjsr305-java
176s   libjung-free-java libkpathsea6 liblapack3 liblatex-tounicode-perl liblcms2-2
176s   liblerc4 liblightcouch-java liblog4j2-java liblsan0 liblua5.4-0
176s   liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto7t64
176s   libmbedtls14t64 libmbedx509-1t64 libmjson-java libmongodb-java libmpfi0
176s   libncbi-ngs3 libncbi-vdb3 libnet-http-perl libnet-ssleay-perl libngs-java
176s   libngs-jni libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
176s   libpaper-utils libpaper1 libpcsclite1 libpicard-java libpixman-1-0
176s   libpotrace0 libprotobuf32t64 libptexenc1 librhino-java libsharpyuv0
176s   libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5
176s   libstaden-read14t64 libstdc++-14-dev libsynctex2 libtbb12 libtbbbind-2-5
176s   libtbbmalloc2 libtcl8.6 libteckit0 libtexlua53-5 libthai-data libthai0
176s   libtiff6 libtimedate-perl libtk8.6 libtry-tiny-perl libtsan2 libubsan1
176s   liburi-perl libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1
176s   libwayland-server0 libwebp7 libwww-perl libwww-robotrules-perl libx11-xcb1
176s   libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0
176s   libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0
176s   libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6
176s   libxinerama1 libxmu6 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxss1
176s   libxt6t64 libxtst6 libxxf86vm1 libzzip-0-13t64 littler mesa-libgallium
176s   ncbi-blast+ ncbi-data ncbi-vdb-data node-bootstrap-sass node-html5shiv
176s   node-normalize.css openjdk-21-jre openjdk-21-jre-headless pandoc pandoc-data
176s   parafly perl-openssl-defaults python3-hisat2 python3-htseq python3-numpy
176s   python3-pysam r-base-core r-bioc-annotate r-bioc-annotationdbi
176s   r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio
176s   r-bioc-biocparallel r-bioc-biocstyle r-bioc-biocversion r-bioc-biomart
176s   r-bioc-biostrings r-bioc-delayedarray r-bioc-deseq2 r-bioc-dexseq
176s   r-bioc-edger r-bioc-genefilter r-bioc-genelendatabase r-bioc-geneplotter
176s   r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments
176s   r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-go.db r-bioc-goseq
176s   r-bioc-iranges r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics
176s   r-bioc-qvalue r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer
176s   r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray
176s   r-bioc-summarizedexperiment r-bioc-txdbmaker r-bioc-ucsc.utils
176s   r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-argparse r-cran-askpass
176s   r-cran-backports r-cran-base64enc r-cran-bh r-cran-biasedurn
176s   r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob
176s   r-cran-bookdown r-cran-broom r-cran-bslib r-cran-cachem r-cran-callr
176s   r-cran-cellranger r-cran-cli r-cran-clipr r-cran-cluster r-cran-codetools
176s   r-cran-colorspace r-cran-commonmark r-cran-conflicted r-cran-cpp11
176s   r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi r-cran-dbplyr
176s   r-cran-digest r-cran-dplyr r-cran-dtplyr r-cran-ellipsis r-cran-evaluate
176s   r-cran-fansi r-cran-farver r-cran-fastcluster r-cran-fastmap r-cran-filelock
176s   r-cran-findpython r-cran-fontawesome r-cran-forcats r-cran-formatr r-cran-fs
176s   r-cran-futile.logger r-cran-futile.options r-cran-gargle r-cran-generics
176s   r-cran-ggdendro r-cran-ggplot2 r-cran-glue r-cran-googledrive
176s   r-cran-googlesheets4 r-cran-goplot r-cran-gridextra r-cran-gtable
176s   r-cran-haven r-cran-highr r-cran-hms r-cran-htmltools r-cran-httpuv
176s   r-cran-httr r-cran-httr2 r-cran-hwriter r-cran-ids r-cran-isoband
176s   r-cran-jquerylib r-cran-jsonlite r-cran-kernsmooth r-cran-knitr
176s   r-cran-labeling r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lifecycle
176s   r-cran-littler r-cran-locfit r-cran-lubridate r-cran-magrittr r-cran-mass
176s   r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime
176s   r-cran-modelr r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar
176s   r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-plyr r-cran-png
176s   r-cran-prettyunits r-cran-processx r-cran-progress r-cran-promises r-cran-ps
176s   r-cran-purrr r-cran-r6 r-cran-ragg r-cran-rappdirs r-cran-rcolorbrewer
176s   r-cran-rcpp r-cran-rcpparmadillo r-cran-rcurl r-cran-readr r-cran-readxl
176s   r-cran-rematch r-cran-rematch2 r-cran-reprex r-cran-reshape2 r-cran-restfulr
176s   r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-rstudioapi
176s   r-cran-rvest r-cran-sass r-cran-scales r-cran-selectr r-cran-shiny
176s   r-cran-snow r-cran-sourcetools r-cran-statmod r-cran-stringi r-cran-stringr
176s   r-cran-survival r-cran-sys r-cran-systemfonts r-cran-textshaping
176s   r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tidyverse
176s   r-cran-timechange r-cran-tinytex r-cran-tzdb r-cran-utf8 r-cran-uuid
176s   r-cran-vctrs r-cran-viridislite r-cran-vroom r-cran-withr r-cran-xfun
176s   r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml rsem salmon samtools
176s   subread t1utils tex-common texlive-base texlive-bibtex-extra
176s   texlive-binaries texlive-latex-base trimmomatic trinityrnaseq
176s   trinityrnaseq-examples ubuntu-mono unzip x11-common xdg-utils zip zlib1g-dev
176s Suggested packages:
176s   bowtie-examples bowtie2-examples apache2 | lighttpd | httpd alsa-utils
176s   libasound2-plugins libatinject-jsr330-api-java-doc libboost-doc
176s   libboost1.83-doc libboost-atomic1.83-dev libboost-chrono1.83-dev
176s   libboost-container1.83-dev libboost-context1.83-dev
176s   libboost-contract1.83-dev libboost-coroutine1.83-dev
176s   libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev
176s   libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev
176s   libboost-graph1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev
176s   libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev
176s   libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev
176s   libboost-numpy1.83-dev libboost-program-options1.83-dev
176s   libboost-python1.83-dev libboost-random1.83-dev libboost-regex1.83-dev
176s   libboost-serialization1.83-dev libboost-stacktrace1.83-dev
176s   libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev
176s   libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev
176s   libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev
176s   colord libasm-java libxz-java libavalon-framework-java
176s   libexcalibur-logkit-java liblog4j1.2-java cups-common jython libdom4j-java
176s   libjaxen-java libjdom1-java libxalan2-java libgoogle-gson-java-doc gvfs
176s   libdata-dump-perl picard-tools libio-compress-brotli-perl
176s   libjoptsimple-java-doc libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix
176s   libjs-mathjax-doc libjsr305-java-doc liblcms2-utils libactivation-java
176s   libcommons-csv-java libconversant-disruptor-java libdisruptor-java
176s   libgeronimo-jms-1.1-spec-java libjackson2-dataformat-xml-java
176s   libjackson2-dataformat-yaml libjansi-java libjctools-java libjeromq-java
176s   libmail-java libwoodstox-java libcrypt-ssleay-perl libmpfi-doc
176s   libngs-java-doc pcscd rhino libstdc++-14-doc tcl8.6 tk8.6 libsub-name-perl
176s   libbusiness-isbn-perl libmime-base32-perl libregexp-ipv6-perl
176s   libauthen-ntlm-perl nodejs libnss-mdns fonts-dejavu-extra
176s   fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei
176s   | fonts-wqy-zenhei fonts-indic texlive-latex-recommended texlive-xetex
176s   texlive-luatex pandoc-citeproc texlive-latex-extra context wkhtmltopdf
176s   librsvg2-bin groff ghc php python ruby libjs-katex
176s   citation-style-language-styles debhelper gcc gfortran python-numpy-doc
176s   python3-dev python3-pytest elpa-ess r-doc-info | r-doc-pdf r-mathlib
176s   r-base-html r-bioc-org.hs.eg.db r-cran-runit r-bioc-graph r-bioc-all
176s   r-cran-testthat r-bioc-affy r-cran-foreach r-cran-bbmisc r-cran-doparallel
176s   r-bioc-variantannotation r-bioc-shortread r-cran-batchtools r-cran-mockery
176s   r-cran-httptest2 r-bioc-bsgenome r-bioc-pwalign r-bioc-hdf5array
176s   r-cran-lobstr r-bioc-delayedmatrixstats r-cran-pheatmap r-bioc-tximport
176s   r-bioc-tximeta r-bioc-tximportdata r-cran-pbapply r-bioc-glmgampoi
176s   r-cran-roxygen2 r-bioc-rhdf5 r-cran-seuratobject r-cran-class r-cran-r.utils
176s   r-bioc-ensembldb r-bioc-annotationfilter r-cran-markdown r-bioc-gviz
176s   r-bioc-annotationhub r-cran-ellipse r-cran-gplots r-bioc-sparsematrixstats
176s   r-cran-rmariadb r-cran-ff r-cran-covr r-cran-kernlab r-cran-mvtnorm
176s   r-cran-vcd r-cran-shinyjs r-cran-jpeg r-cran-viridis r-cran-rmysql
176s   r-cran-bench r-cran-waldo r-cran-reticulate r-cran-spelling r-cran-magick
176s   r-cran-sf r-cran-getopt r-cran-interp r-cran-gam r-cran-formattable
176s   r-cran-nanotime r-cran-palmerpenguins r-cran-units r-cran-vdiffr
176s   r-cran-inline r-cran-rmpi r-cran-rlecuyer r-cran-brio r-cran-here
176s   r-cran-pkgbuild r-cran-pkgload r-cran-mockr r-cran-plm r-cran-zoo
176s   r-bioc-ebseq cwltool ghostscript gv | postscript-viewer perl-tk xpdf
176s   | pdf-viewer xzdec texlive-binaries-sse2 hintview texlive-latex-base-doc
176s   wp2latex collectl transdecoder
176s Recommended packages:
176s   librsvg2-common med-config bcftools alsa-ucm-conf alsa-topology-conf
176s   at-spi2-core libgdk-pixbuf2.0-bin libgkl-jni libgl1-amber-dri libgtk-3-bin
176s   libhtml-format-perl libhwloc-plugins node-jquery mesa-vulkan-drivers
176s   | vulkan-icd libdata-dump-perl libhtml-form-perl libhttp-daemon-perl
176s   libmailtools-perl libatk-wrapper-java-jni fonts-dejavu-extra r-recommended
176s   r-base-dev r-doc-html r-cran-testthat r-cran-remotes r-cran-downlit
176s   r-cran-htmlwidgets r-cran-miniui r-cran-rsconnect r-cran-testit r-cran-tufte
176s   r-cran-webshot r-cran-aer r-cran-bbmle r-cran-boot r-cran-car r-cran-cardata
176s   r-cran-caret r-cran-cmprsk r-cran-coda r-cran-covr r-cran-e1071
176s   r-cran-emmeans r-cran-epir r-cran-gam r-cran-gee r-cran-geepack
176s   r-cran-glmnet r-cran-gmm r-cran-hmisc r-cran-irlba r-cran-interp r-cran-ks
176s   r-cran-lavaan r-cran-leaps r-cran-lme4 r-cran-lmtest r-cran-lsmeans
176s   r-cran-maps r-cran-mclust r-cran-metafor r-cran-modeldata r-cran-multcomp
176s   r-cran-network r-cran-nnet r-cran-ordinal r-cran-plm r-cran-psych
176s   r-cran-quantreg r-cran-robust r-cran-robustbase r-cran-rsample
176s   r-cran-sandwich r-cran-spdep r-cran-spatialreg r-cran-spelling r-cran-survey
176s   r-cran-systemfit r-cran-tseries r-cran-zoo r-cran-future r-cran-thematic
176s   r-cran-mockery r-cran-rprojroot r-cran-whoami r-cran-pkgload r-cran-bench
176s   r-cran-brio r-cran-decor r-cran-desc r-cran-lobstr r-cran-webutils
176s   r-cran-r.utils r-cran-xts r-cran-markdown r-cran-rpostgresql r-cran-rmysql
176s   r-cran-unitizer r-cran-rsvg r-cran-sodium r-cran-rpart r-cran-hexbin
176s   r-cran-mapproj r-cran-profvis r-cran-sf r-cran-svglite r-cran-vdiffr
176s   r-cran-waldo r-cran-mockr r-cran-cairo r-cran-jpeg r-cran-docopt
176s   r-cran-webfakes r-cran-r.rsp r-cran-gridsvg r-cran-magick r-cran-reticulate
176s   r-cran-rgl r-cran-tikzdevice node-highlight.js r-cran-lintr r-cran-r.devices
176s   r-cran-doparallel r-cran-foreach r-cran-iterators r-cran-itertools
176s   r-cran-pingr r-cran-sessioninfo r-cran-runit r-cran-usethis r-cran-dygraphs
176s   r-cran-dbitest r-cran-gert r-cran-gh r-cran-dichromat r-cran-dt
176s   r-cran-formattable r-cran-pkgdown r-cran-zeallot r-cran-renv lmodern dvisvgm
176s   picard-tools tabix gmap rna-star r-bioc-rots r-bioc-ctc r-cran-gplots
176s   r-cran-ape libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl
176s   x11-utils x11-xserver-utils
176s The following NEW packages will be installed:
176s   adwaita-icon-theme at-spi2-common autopkgtest-satdep berkeley-express bowtie
176s   bowtie2 ca-certificates-java dconf-gsettings-backend dconf-service
176s   default-jre default-jre-headless fontconfig fontconfig-config
176s   fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome
176s   fonts-glyphicons-halflings fonts-lmodern fonts-mathjax gtk-update-icon-cache
176s   hicolor-icon-theme hisat2 humanity-icon-theme jaligner java-common
176s   javascript-common jellyfish kallisto libapache-pom-java libasan8
176s   libasound2-data libasound2t64 libatinject-jsr330-api-java
176s   libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 libavahi-client3
176s   libavahi-common-data libavahi-common3 libbamtools2.5.2 libbarclay-java
176s   libbibtex-parser-perl libblas3 libboost-dev libboost-filesystem1.83.0
176s   libboost-iostreams1.83.0 libboost-program-options1.83.0
176s   libboost-thread1.83.0 libboost1.83-dev libcairo-gobject2 libcairo2
176s   libclone-perl libcolord2 libcommons-codec-java libcommons-compress-java
176s   libcommons-io-java libcommons-jexl2-java libcommons-lang3-java
176s   libcommons-logging-java libcommons-math3-java libcommons-parent-java
176s   libcups2t64 libdatrie1 libdconf1 libdeflate0 libdrm-amdgpu1 libdrm-radeon1
176s   libencode-locale-perl libepoxy0 liberror-prone-java libfile-listing-perl
176s   libfontconfig1 libfreemarker-java libgatk-native-bindings-java libgbm1
176s   libgcc-14-dev libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgetopt-java
176s   libgfortran5 libgif7 libgkl-java libgl1 libgl1-mesa-dri libglapi-mesa
176s   libglvnd0 libglx-mesa0 libglx0 libgomp1 libgoogle-gson-java libgraphite2-3
176s   libgtk-3-0t64 libgtk-3-common libguava-java libharfbuzz0b
176s   libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts3t64
176s   libhtscodecs2 libhtsjdk-java libhttp-cookies-perl libhttp-date-perl
176s   libhttp-message-perl libhttp-negotiate-perl libhttpclient-java
176s   libhttpcore-java libhwasan0 libhwloc15 libice6 libio-html-perl
176s   libio-socket-ssl-perl libio-string-perl libitm1 libjbig0 libjbzip2-java
176s   libjellyfish-2.0-2 libjemalloc2 libjoptsimple-java libjpeg-turbo8 libjpeg8
176s   libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js
176s   libjs-jquery libjs-jquery-datatables libjs-jquery-selectize.js
176s   libjs-jquery-ui libjs-json libjs-lunr libjs-mathjax libjs-microplugin.js
176s   libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js
176s   libjs-sphinxdoc libjs-twitter-bootstrap-datepicker libjs-underscore
176s   libjsr305-java libjung-free-java libkpathsea6 liblapack3
176s   liblatex-tounicode-perl liblcms2-2 liblerc4 liblightcouch-java
176s   liblog4j2-java liblsan0 liblua5.4-0 liblwp-mediatypes-perl
176s   liblwp-protocol-https-perl libmbedcrypto7t64 libmbedtls14t64
176s   libmbedx509-1t64 libmjson-java libmongodb-java libmpfi0 libncbi-ngs3
176s   libncbi-vdb3 libnet-http-perl libnet-ssleay-perl libngs-java libngs-jni
176s   libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
176s   libpaper1 libpcsclite1 libpicard-java libpixman-1-0 libpotrace0
176s   libprotobuf32t64 libptexenc1 librhino-java libsharpyuv0 libslf4j-java libsm6
176s   libsnappy-java libsnappy-jni libsnappy1v5 libstaden-read14t64
176s   libstdc++-14-dev libsynctex2 libtbb12 libtbbbind-2-5 libtbbmalloc2 libtcl8.6
176s   libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6 libtimedate-perl
176s   libtk8.6 libtry-tiny-perl libtsan2 libubsan1 liburi-perl libvulkan1
176s   libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0
176s   libwebp7 libwww-perl libwww-robotrules-perl libx11-xcb1 libxaw7
176s   libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0
176s   libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcomposite1
176s   libxcursor1 libxdamage1 libxfixes3 libxft2 libxi6 libxinerama1 libxmu6
176s   libxpm4 libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6t64 libxtst6
176s   libxxf86vm1 libzzip-0-13t64 littler mesa-libgallium ncbi-blast+ ncbi-data
176s   ncbi-vdb-data node-bootstrap-sass node-html5shiv node-normalize.css
176s   openjdk-21-jre openjdk-21-jre-headless pandoc pandoc-data parafly
176s   perl-openssl-defaults python3-hisat2 python3-htseq python3-numpy
176s   python3-pysam r-base-core r-bioc-annotate r-bioc-annotationdbi
176s   r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio
176s   r-bioc-biocparallel r-bioc-biocstyle r-bioc-biocversion r-bioc-biomart
176s   r-bioc-biostrings r-bioc-delayedarray r-bioc-deseq2 r-bioc-dexseq
176s   r-bioc-edger r-bioc-genefilter r-bioc-genelendatabase r-bioc-geneplotter
176s   r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments
176s   r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-go.db r-bioc-goseq
176s   r-bioc-iranges r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics
176s   r-bioc-qvalue r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer
176s   r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray
176s   r-bioc-summarizedexperiment r-bioc-txdbmaker r-bioc-ucsc.utils
176s   r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-argparse r-cran-askpass
176s   r-cran-backports r-cran-base64enc r-cran-bh r-cran-biasedurn
176s   r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob
176s   r-cran-bookdown r-cran-broom r-cran-bslib r-cran-cachem r-cran-callr
176s   r-cran-cellranger r-cran-cli r-cran-clipr r-cran-cluster r-cran-codetools
176s   r-cran-colorspace r-cran-commonmark r-cran-conflicted r-cran-cpp11
176s   r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi r-cran-dbplyr
176s   r-cran-digest r-cran-dplyr r-cran-dtplyr r-cran-ellipsis r-cran-evaluate
176s   r-cran-fansi r-cran-farver r-cran-fastcluster r-cran-fastmap r-cran-filelock
176s   r-cran-findpython r-cran-fontawesome r-cran-forcats r-cran-formatr r-cran-fs
176s   r-cran-futile.logger r-cran-futile.options r-cran-gargle r-cran-generics
176s   r-cran-ggdendro r-cran-ggplot2 r-cran-glue r-cran-googledrive
176s   r-cran-googlesheets4 r-cran-goplot r-cran-gridextra r-cran-gtable
176s   r-cran-haven r-cran-highr r-cran-hms r-cran-htmltools r-cran-httpuv
176s   r-cran-httr r-cran-httr2 r-cran-hwriter r-cran-ids r-cran-isoband
176s   r-cran-jquerylib r-cran-jsonlite r-cran-kernsmooth r-cran-knitr
176s   r-cran-labeling r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lifecycle
176s   r-cran-littler r-cran-locfit r-cran-lubridate r-cran-magrittr r-cran-mass
176s   r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime
176s   r-cran-modelr r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar
176s   r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-plyr r-cran-png
176s   r-cran-prettyunits r-cran-processx r-cran-progress r-cran-promises r-cran-ps
176s   r-cran-purrr r-cran-r6 r-cran-ragg r-cran-rappdirs r-cran-rcolorbrewer
176s   r-cran-rcpp r-cran-rcpparmadillo r-cran-rcurl r-cran-readr r-cran-readxl
176s   r-cran-rematch r-cran-rematch2 r-cran-reprex r-cran-reshape2 r-cran-restfulr
176s   r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-rstudioapi
176s   r-cran-rvest r-cran-sass r-cran-scales r-cran-selectr r-cran-shiny
176s   r-cran-snow r-cran-sourcetools r-cran-statmod r-cran-stringi r-cran-stringr
176s   r-cran-survival r-cran-sys r-cran-systemfonts r-cran-textshaping
176s   r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tidyverse
176s   r-cran-timechange r-cran-tinytex r-cran-tzdb r-cran-utf8 r-cran-uuid
176s   r-cran-vctrs r-cran-viridislite r-cran-vroom r-cran-withr r-cran-xfun
176s   r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml rsem salmon samtools
176s   subread t1utils tex-common texlive-base texlive-bibtex-extra
176s   texlive-binaries texlive-latex-base trimmomatic trinityrnaseq
176s   trinityrnaseq-examples ubuntu-mono unzip x11-common xdg-utils zip zlib1g-dev
176s 0 upgraded, 471 newly installed, 0 to remove and 0 not upgraded.
176s Need to get 983 MB/983 MB of archives.
176s After this operation, 2412 MB of additional disk space will be used.
176s Get:1 /tmp/autopkgtest.xkSdGF/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [828 B]
176s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [7888 B]
176s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB]
176s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
176s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.21-1 [46.2 kB]
176s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
176s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB]
176s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB]
176s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB]
176s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB]
176s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-1 [145 kB]
176s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 gtk-update-icon-cache arm64 4.16.2+ds-2 [51.1 kB]
176s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 hicolor-icon-theme all 0.18-1 [13.5 kB]
176s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 humanity-icon-theme all 0.6.16 [1282 kB]
177s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 ubuntu-mono all 24.04-0ubuntu1 [151 kB]
177s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 adwaita-icon-theme all 47.0-1 [525 kB]
177s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 at-spi2-common all 2.54.0-1 [8774 B]
177s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 libbamtools2.5.2 arm64 2.5.2+dfsg-6 [132 kB]
177s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-filesystem1.83.0 arm64 1.83.0-3.2ubuntu2 [282 kB]
177s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-program-options1.83.0 arm64 1.83.0-3.2ubuntu2 [318 kB]
177s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-thread1.83.0 arm64 1.83.0-3.2ubuntu2 [276 kB]
177s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libprotobuf32t64 arm64 3.21.12-9ubuntu1 [868 kB]
177s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 berkeley-express arm64 1.5.3+dfsg-3build5 [213 kB]
177s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 ca-certificates-java all 20240118 [11.6 kB]
177s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libdconf1 arm64 0.40.0-4build2 [39.8 kB]
177s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 dconf-service arm64 0.40.0-4build2 [26.9 kB]
177s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 dconf-gsettings-backend arm64 0.40.0-4build2 [22.0 kB]
177s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 java-common all 0.76 [6852 B]
177s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.14-2build1 [161 kB]
177s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcsclite1 arm64 2.3.0-1 [24.4 kB]
177s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 openjdk-21-jre-headless arm64 21.0.5+11-1 [45.7 MB]
179s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 default-jre-headless arm64 2:1.21-76 [3176 B]
179s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libatk1.0-0t64 arm64 2.54.0-1 [55.0 kB]
179s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB]
179s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libatspi2.0-0t64 arm64 2.54.0-1 [80.2 kB]
179s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libatk-bridge2.0-0t64 arm64 2.54.0-1 [66.6 kB]
179s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
179s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
179s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB]
179s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB]
179s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.42.2-1build1 [204 kB]
179s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB]
179s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B]
179s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB]
179s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB]
179s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo-gobject2 arm64 1.18.2-2 [127 kB]
179s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libcolord2 arm64 1.4.7-1build2 [149 kB]
179s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-common-data arm64 0.8-13ubuntu6 [29.6 kB]
179s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-common3 arm64 0.8-13ubuntu6 [23.3 kB]
179s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-client3 arm64 0.8-13ubuntu6 [27.2 kB]
179s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libcups2t64 arm64 2.4.10-1ubuntu2 [271 kB]
179s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libepoxy0 arm64 1.5.10-1build1 [240 kB]
179s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
179s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 9.0.0-1 [486 kB]
179s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-1.1ubuntu2 [190 kB]
179s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB]
179s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB]
179s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB]
179s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.54.0+ds-2 [233 kB]
179s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.54.0+ds-2 [48.8 kB]
179s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.54.0+ds-2 [27.5 kB]
179s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-client0 arm64 1.23.0-1 [26.7 kB]
179s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-cursor0 arm64 1.23.0-1 [10.6 kB]
179s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-egl1 arm64 1.23.0-1 [5636 B]
179s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcomposite1 arm64 1:0.4.5-1build3 [6336 B]
179s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 libxfixes3 arm64 1:6.0.0-2build1 [11.2 kB]
179s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcursor1 arm64 1:1.2.2-1 [21.2 kB]
179s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libxdamage1 arm64 1:1.1.6-1build1 [6236 B]
179s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libxinerama1 arm64 2:1.1.4-3build1 [6394 B]
179s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrandr2 arm64 2:1.5.4-1 [19.6 kB]
179s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libgtk-3-common all 3.24.43-3ubuntu2 [1202 kB]
179s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libgtk-3-0t64 arm64 3.24.43-3ubuntu2 [2898 kB]
179s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libglvnd0 arm64 1.7.0-1build1 [60.6 kB]
179s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libglapi-mesa arm64 24.2.3-1ubuntu1 [59.4 kB]
179s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libx11-xcb1 arm64 2:1.8.7-1build1 [7870 B]
179s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-dri2-0 arm64 1.17.0-2 [7418 B]
179s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-dri3-0 arm64 1.17.0-2 [7606 B]
179s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-glx0 arm64 1.17.0-2 [25.5 kB]
179s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-present0 arm64 1.17.0-2 [6224 B]
179s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-randr0 arm64 1.17.0-2 [18.5 kB]
179s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-sync1 arm64 1.17.0-2 [9688 B]
179s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-xfixes0 arm64 1.17.0-2 [10.6 kB]
179s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 libxshmfence1 arm64 1.3-1build5 [4938 B]
179s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libxxf86vm1 arm64 1:1.1.4-1build4 [9130 B]
179s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libdrm-amdgpu1 arm64 2.4.122-1 [20.9 kB]
179s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 libdrm-radeon1 arm64 2.4.122-1 [20.8 kB]
179s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 mesa-libgallium arm64 24.2.3-1ubuntu1 [9030 kB]
179s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 libvulkan1 arm64 1.3.290.0-1 [153 kB]
179s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 libwayland-server0 arm64 1.23.0-1 [35.7 kB]
179s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 libgbm1 arm64 24.2.3-1ubuntu1 [32.9 kB]
179s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 libgl1-mesa-dri arm64 24.2.3-1ubuntu1 [33.3 kB]
179s Get:92 http://ftpmaster.internal/ubuntu plucky/main arm64 libglx-mesa0 arm64 24.2.3-1ubuntu1 [164 kB]
179s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 libglx0 arm64 1.7.0-1build1 [33.2 kB]
179s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 libgl1 arm64 1.7.0-1build1 [106 kB]
179s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 libasound2-data all 1.2.12-1 [21.0 kB]
179s Get:96 http://ftpmaster.internal/ubuntu plucky/main arm64 libasound2t64 arm64 1.2.12-1 [384 kB]
179s Get:97 http://ftpmaster.internal/ubuntu plucky/main arm64 libgif7 arm64 5.2.2-1ubuntu1 [35.5 kB]
180s Get:98 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
180s Get:99 http://ftpmaster.internal/ubuntu plucky/main arm64 libxtst6 arm64 2:1.2.3-1.1build1 [13.0 kB]
180s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 openjdk-21-jre arm64 21.0.5+11-1 [221 kB]
180s Get:101 http://ftpmaster.internal/ubuntu plucky/main arm64 default-jre arm64 2:1.21-76 [918 B]
180s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB]
180s Get:103 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB]
180s Get:104 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lmodern all 2.005-1 [4799 kB]
180s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
180s Get:106 http://ftpmaster.internal/ubuntu plucky/universe arm64 hisat2 arm64 2.2.1-5 [3961 kB]
181s Get:107 http://ftpmaster.internal/ubuntu plucky/universe arm64 jaligner all 1.0+dfsg-11 [136 kB]
181s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 javascript-common all 11+nmu1 [5936 B]
181s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.0-1build1 [78.0 kB]
181s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-1 [431 kB]
181s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjellyfish-2.0-2 arm64 2.3.1-3build2 [66.0 kB]
181s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 jellyfish arm64 2.3.1-3build2 [728 kB]
181s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 kallisto arm64 0.48.0+dfsg-4build1 [256 kB]
181s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 libapache-pom-java all 29-2 [5284 B]
181s Get:115 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 14.2.0-7ubuntu1 [2893 kB]
181s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 libatinject-jsr330-api-java all 1.0+ds1-5 [5348 B]
181s Get:117 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-parent-java all 56-1 [10.7 kB]
181s Get:118 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-lang3-java all 3.14.0-1 [586 kB]
181s Get:119 http://ftpmaster.internal/ubuntu plucky/universe arm64 libfreemarker-java all 2.3.32-2 [1542 kB]
181s Get:120 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgoogle-gson-java all 2.10.1-1 [252 kB]
181s Get:121 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjoptsimple-java all 5.0.4-4 [73.1 kB]
181s Get:122 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-codec-java all 1.16.0-1 [306 kB]
181s Get:123 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB]
181s Get:124 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhttpcore-java all 4.4.16-1 [612 kB]
181s Get:125 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhttpclient-java all 4.5.14-1 [1241 kB]
181s Get:126 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblightcouch-java all 0.2.0-1 [74.2 kB]
181s Get:127 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmongodb-java all 3.6.3-2 [1899 kB]
181s Get:128 http://ftpmaster.internal/ubuntu plucky/universe arm64 libslf4j-java all 1.7.32-1 [141 kB]
181s Get:129 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblog4j2-java all 2.19.0-2 [2294 kB]
181s Get:130 http://ftpmaster.internal/ubuntu plucky/universe arm64 libbarclay-java all 5.0.0+dfsg-1 [108 kB]
181s Get:131 http://ftpmaster.internal/ubuntu plucky/main arm64 libio-string-perl all 1.08-4 [11.1 kB]
181s Get:132 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblatex-tounicode-perl all 0.54-2 [29.0 kB]
181s Get:133 http://ftpmaster.internal/ubuntu plucky/universe arm64 libbibtex-parser-perl all 1.04+dfsg-1 [16.7 kB]
181s Get:134 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB]
181s Get:135 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-7ubuntu1 [145 kB]
181s Get:136 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 14.2.0-7ubuntu1 [27.8 kB]
181s Get:137 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 14.2.0-7ubuntu1 [1283 kB]
181s Get:138 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 14.2.0-7ubuntu1 [2691 kB]
181s Get:139 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 14.2.0-7ubuntu1 [1151 kB]
182s Get:140 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 14.2.0-7ubuntu1 [1599 kB]
182s Get:141 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-7ubuntu1 [2594 kB]
182s Get:142 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-7ubuntu1 [2474 kB]
182s Get:143 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost1.83-dev arm64 1.83.0-3.2ubuntu2 [10.7 MB]
182s Get:144 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-dev arm64 1.83.0.2ubuntu1 [4468 B]
182s Get:145 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-3.2ubuntu2 [259 kB]
182s Get:146 http://ftpmaster.internal/ubuntu plucky/main arm64 libclone-perl arm64 0.47-1 [10.4 kB]
182s Get:147 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-compress-java all 1.25.0-1 [612 kB]
182s Get:148 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-io-java all 2.16.1-1 [451 kB]
182s Get:149 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-jexl2-java all 2.1.1-6 [250 kB]
182s Get:150 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-math3-java all 3.6.1-3 [2016 kB]
182s Get:151 http://ftpmaster.internal/ubuntu plucky/main arm64 libencode-locale-perl all 1.05-3 [11.6 kB]
182s Get:152 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjsr305-java all 0.1~+svn49-11 [27.0 kB]
182s Get:153 http://ftpmaster.internal/ubuntu plucky/universe arm64 libguava-java all 32.0.1-1 [2692 kB]
183s Get:154 http://ftpmaster.internal/ubuntu plucky/universe arm64 liberror-prone-java all 2.18.0-1 [22.5 kB]
183s Get:155 http://ftpmaster.internal/ubuntu plucky/main arm64 libtimedate-perl all 2.3300-2 [34.0 kB]
183s Get:156 http://ftpmaster.internal/ubuntu plucky/main arm64 libhttp-date-perl all 6.06-1 [10.2 kB]
183s Get:157 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-listing-perl all 6.16-1 [11.3 kB]
183s Get:158 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8014 B]
183s Get:159 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgetopt-java all 1.0.14+dfsg-6 [23.0 kB]
183s Get:160 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-7ubuntu1 [438 kB]
183s Get:161 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmjson-java all 1.4.0-3 [60.4 kB]
183s Get:162 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmbedcrypto7t64 arm64 2.28.8-1 [209 kB]
183s Get:163 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmbedx509-1t64 arm64 2.28.8-1 [47.2 kB]
183s Get:164 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmbedtls14t64 arm64 2.28.8-1 [82.2 kB]
183s Get:165 http://ftpmaster.internal/ubuntu plucky/universe arm64 ncbi-vdb-data all 3.0.2+dfsg-2build2 [67.5 kB]
183s Get:166 http://ftpmaster.internal/ubuntu plucky/universe arm64 libncbi-vdb3 arm64 3.0.2+dfsg-2build2 [1143 kB]
183s Get:167 http://ftpmaster.internal/ubuntu plucky/universe arm64 libncbi-ngs3 arm64 3.0.3+dfsg-9ubuntu1 [145 kB]
183s Get:168 http://ftpmaster.internal/ubuntu plucky/universe arm64 libngs-jni arm64 3.0.3+dfsg-9ubuntu1 [4844 B]
183s Get:169 http://ftpmaster.internal/ubuntu plucky/universe arm64 libngs-java arm64 3.0.3+dfsg-9ubuntu1 [91.1 kB]
183s Get:170 http://ftpmaster.internal/ubuntu plucky/universe arm64 librhino-java all 1.7.14-2.1 [1330 kB]
183s Get:171 http://ftpmaster.internal/ubuntu plucky/main arm64 libsnappy1v5 arm64 1.2.1-1 [30.4 kB]
183s Get:172 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsnappy-jni arm64 1.1.10.5-2 [6618 B]
183s Get:173 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsnappy-java all 1.1.10.5-2 [83.7 kB]
183s Get:174 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtsjdk-java all 4.1.0+dfsg-2 [1823 kB]
183s Get:175 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgkl-java all 0.8.11+dfsg-2build1 [24.9 kB]
183s Get:176 http://ftpmaster.internal/ubuntu plucky/main arm64 libhtml-tagset-perl all 3.24-1 [14.1 kB]
183s Get:177 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 liburi-perl all 5.30-1 [94.4 kB]
183s Get:178 http://ftpmaster.internal/ubuntu plucky/main arm64 libhtml-parser-perl arm64 3.83-1build1 [85.3 kB]
183s Get:179 http://ftpmaster.internal/ubuntu plucky/main arm64 libhtml-tree-perl all 5.07-3 [200 kB]
183s Get:180 http://ftpmaster.internal/ubuntu plucky/main arm64 libio-html-perl all 1.004-3 [15.9 kB]
183s Get:181 http://ftpmaster.internal/ubuntu plucky/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.1 kB]
183s Get:182 http://ftpmaster.internal/ubuntu plucky/main arm64 libhttp-message-perl all 6.46-1ubuntu1 [75.9 kB]
183s Get:183 http://ftpmaster.internal/ubuntu plucky/main arm64 libhttp-cookies-perl all 6.11-1 [18.2 kB]
183s Get:184 http://ftpmaster.internal/ubuntu plucky/main arm64 libhttp-negotiate-perl all 6.01-2 [12.4 kB]
183s Get:185 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc15 arm64 2.11.0-2 [160 kB]
183s Get:186 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.0.10-1build3 [41.1 kB]
183s Get:187 http://ftpmaster.internal/ubuntu plucky/main arm64 perl-openssl-defaults arm64 7build3 [6628 B]
183s Get:188 http://ftpmaster.internal/ubuntu plucky/main arm64 libnet-ssleay-perl arm64 1.94-2 [307 kB]
183s Get:189 http://ftpmaster.internal/ubuntu plucky/main arm64 libio-socket-ssl-perl all 2.088-1 [200 kB]
183s Get:190 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjemalloc2 arm64 5.3.0-2build1 [204 kB]
183s Get:191 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB]
183s Get:192 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-popper.js all 1.16.1+ds-6 [54.1 kB]
183s Get:193 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [537 kB]
183s Get:194 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-d3 all 3.5.17-4 [132 kB]
183s Get:195 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-es5-shim all 4.6.7-2 [39.8 kB]
183s Get:196 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB]
183s Get:197 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
183s Get:198 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB]
183s Get:199 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB]
183s Get:200 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3712 B]
183s Get:201 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB]
183s Get:202 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
183s Get:203 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-json all 0~20221030+~1.0.8-1 [20.6 kB]
183s Get:204 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-lunr all 2.3.9~dfsg-2 [66.8 kB]
183s Get:205 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-prettify all 2015.12.04+dfsg-1.1 [39.3 kB]
183s Get:206 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
184s Get:207 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-3 [157 kB]
184s Get:208 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjung-free-java all 2.1.1-2 [1471 kB]
184s Get:209 http://ftpmaster.internal/ubuntu plucky/main arm64 libkpathsea6 arm64 2024.20240313.70630+ds-4 [64.0 kB]
184s Get:210 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB]
184s Get:211 http://ftpmaster.internal/ubuntu plucky/main arm64 liblua5.4-0 arm64 5.4.6-3build2 [158 kB]
184s Get:212 http://ftpmaster.internal/ubuntu plucky/main arm64 libnet-http-perl all 6.23-1 [22.3 kB]
184s Get:213 http://ftpmaster.internal/ubuntu plucky/main arm64 libtry-tiny-perl all 0.31-2 [20.8 kB]
184s Get:214 http://ftpmaster.internal/ubuntu plucky/main arm64 libwww-robotrules-perl all 6.02-1 [12.6 kB]
184s Get:215 http://ftpmaster.internal/ubuntu plucky/main arm64 libwww-perl all 6.77-1 [138 kB]
184s Get:216 http://ftpmaster.internal/ubuntu plucky/main arm64 liblwp-protocol-https-perl all 6.14-1 [9040 B]
184s Get:217 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmpfi0 arm64 1.5.4+ds-3 [34.9 kB]
184s Get:218 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper1 arm64 1.1.29build1 [13.4 kB]
184s Get:219 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 1.1.29build1 [8490 B]
184s Get:220 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpicard-java all 3.1.1+dfsg-1 [1731 kB]
184s Get:221 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpotrace0 arm64 1.16-2build1 [16.0 kB]
184s Get:222 http://ftpmaster.internal/ubuntu plucky/main arm64 libptexenc1 arm64 2024.20240313.70630+ds-4 [41.6 kB]
184s Get:223 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.3-1build3 [15.6 kB]
184s Get:224 http://ftpmaster.internal/ubuntu plucky/universe arm64 libstaden-read14t64 arm64 1.15.0-1.1build2 [248 kB]
184s Get:225 http://ftpmaster.internal/ubuntu plucky/main arm64 libsynctex2 arm64 2024.20240313.70630+ds-4 [60.0 kB]
184s Get:226 http://ftpmaster.internal/ubuntu plucky/universe arm64 libtbbmalloc2 arm64 2021.12.0-1ubuntu2 [38.5 kB]
184s Get:227 http://ftpmaster.internal/ubuntu plucky/universe arm64 libtbbbind-2-5 arm64 2021.12.0-1ubuntu2 [14.9 kB]
184s Get:228 http://ftpmaster.internal/ubuntu plucky/universe arm64 libtbb12 arm64 2021.12.0-1ubuntu2 [68.1 kB]
184s Get:229 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.14+dfsg-1build1 [978 kB]
184s Get:230 http://ftpmaster.internal/ubuntu plucky/universe arm64 libteckit0 arm64 2.5.12+ds1-1 [405 kB]
184s Get:231 http://ftpmaster.internal/ubuntu plucky/main arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-4 [121 kB]
184s Get:232 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB]
184s Get:233 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B]
184s Get:234 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.14-1build1 [767 kB]
184s Get:235 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB]
184s Get:236 http://ftpmaster.internal/ubuntu plucky/main arm64 libxmu6 arm64 2:1.1.3-3build2 [47.5 kB]
184s Get:237 http://ftpmaster.internal/ubuntu plucky/main arm64 libxpm4 arm64 1:3.5.17-1build2 [35.1 kB]
184s Get:238 http://ftpmaster.internal/ubuntu plucky/main arm64 libxaw7 arm64 2:1.0.14-1build2 [183 kB]
184s Get:239 http://ftpmaster.internal/ubuntu plucky/universe arm64 libzzip-0-13t64 arm64 0.13.72+dfsg.1-1.2build1 [29.2 kB]
184s Get:240 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14 [172 kB]
184s Get:241 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB]
184s Get:242 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-0ubuntu1 [67.5 kB]
184s Get:243 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.1-1 [28.3 MB]
185s Get:244 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-littler arm64 0.3.20-1 [96.4 kB]
185s Get:245 http://ftpmaster.internal/ubuntu plucky/universe arm64 littler all 0.3.20-1 [2486 B]
185s Get:246 http://ftpmaster.internal/ubuntu plucky/universe arm64 ncbi-data all 6.1.20170106+dfsg2-3 [3966 kB]
185s Get:247 http://ftpmaster.internal/ubuntu plucky/universe arm64 ncbi-blast+ arm64 2.16.0+ds-6 [14.7 MB]
186s Get:248 http://ftpmaster.internal/ubuntu plucky/universe arm64 node-bootstrap-sass all 3.4.3-2 [187 kB]
186s Get:249 http://ftpmaster.internal/ubuntu plucky/universe arm64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB]
186s Get:250 http://ftpmaster.internal/ubuntu plucky/universe arm64 node-normalize.css all 8.0.1-5 [10.8 kB]
186s Get:251 http://ftpmaster.internal/ubuntu plucky/universe arm64 pandoc-data all 3.1.11.1-3 [78.7 kB]
186s Get:252 http://ftpmaster.internal/ubuntu plucky/universe arm64 pandoc arm64 3.1.11.1+ds-2 [28.1 MB]
187s Get:253 http://ftpmaster.internal/ubuntu plucky/universe arm64 parafly arm64 0.1.0-4 [15.3 kB]
187s Get:254 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-hisat2 all 2.2.1-5 [12.7 kB]
187s Get:255 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB]
187s Get:256 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.22.1+ds-2 [3412 kB]
187s Get:257 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-htseq arm64 2.0.5-2 [303 kB]
187s Get:258 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biocgenerics all 0.50.0-2 [605 kB]
187s Get:259 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biobase arm64 2.64.0-4 [2148 kB]
188s Get:260 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-s4vectors arm64 0.42.1+dfsg-2 [1889 kB]
188s Get:261 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-iranges arm64 2.38.1-1 [2300 kB]
188s Get:262 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-dbi all 1.2.3-1 [853 kB]
188s Get:263 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bit arm64 4.0.5-1 [1057 kB]
188s Get:264 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bit64 arm64 4.0.5-1 [467 kB]
188s Get:265 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rlang arm64 1.1.4-1 [1707 kB]
188s Get:266 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cli arm64 3.6.2-1 [1377 kB]
188s Get:267 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-glue arm64 1.7.0-1 [154 kB]
188s Get:268 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
188s Get:269 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB]
188s Get:270 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-blob all 1.2.4-1 [49.8 kB]
188s Get:271 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fastmap arm64 1.1.1-1 [69.6 kB]
188s Get:272 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cachem arm64 1.0.8-1 [72.3 kB]
188s Get:273 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-memoise all 2.0.1-1 [53.9 kB]
188s Get:274 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
188s Get:275 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-plogr all 0.2.0-3build1 [15.1 kB]
188s Get:276 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cpp11 all 0.4.7-1 [266 kB]
188s Get:277 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rsqlite arm64 2.3.7-2 [1222 kB]
188s Get:278 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-curl arm64 5.2.1+dfsg-1 [179 kB]
188s Get:279 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-jsonlite arm64 1.8.8+dfsg-1 [441 kB]
188s Get:280 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mime arm64 0.12-2 [35.8 kB]
188s Get:281 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-sys arm64 3.4.2-1 [44.3 kB]
188s Get:282 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-askpass arm64 1.2.0-1 [24.4 kB]
188s Get:283 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-openssl arm64 2.2.0+dfsg-1 [404 kB]
188s Get:284 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-r6 all 2.5.1-1 [99.0 kB]
188s Get:285 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
188s Get:286 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-png arm64 0.1-8-1build2 [40.1 kB]
188s Get:287 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB]
188s Get:288 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-zlibbioc all 1.50.0+dfsg-2 [10.1 kB]
188s Get:289 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-xvector arm64 0.44.0-1 [620 kB]
188s Get:290 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-ucsc.utils all 1.0.0+ds-2 [77.0 kB]
188s Get:291 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-genomeinfodbdata all 1.2.12-1 [12.6 MB]
189s Get:292 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-genomeinfodb all 1.40.1+dfsg-1 [3883 kB]
189s Get:293 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-crayon all 1.5.2-1 [164 kB]
189s Get:294 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biostrings arm64 2.72.1+dfsg-1 [13.2 MB]
190s Get:295 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-keggrest all 1.44.1+dfsg-1 [188 kB]
190s Get:296 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-annotationdbi all 1.66.0-1 [4848 kB]
190s Get:297 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-xml arm64 3.99-0.17-1 [1745 kB]
190s Get:298 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-xtable all 1:1.8-4-2 [689 kB]
190s Get:299 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-annotate all 1.82.0+dfsg-1 [1765 kB]
190s Get:300 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-generics all 0.1.3-1 [81.3 kB]
190s Get:301 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB]
190s Get:302 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB]
190s Get:303 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB]
190s Get:304 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB]
190s Get:305 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-2 [415 kB]
190s Get:306 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-withr all 3.0.0+dfsg-1 [228 kB]
190s Get:307 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tidyselect arm64 1.2.1+dfsg-1 [222 kB]
190s Get:308 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-dplyr arm64 1.1.4-1 [1513 kB]
191s Get:309 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-purrr arm64 1.0.2-1 [501 kB]
191s Get:310 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-stringi arm64 1.8.3-1 [869 kB]
191s Get:311 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB]
191s Get:312 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB]
191s Get:313 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-dbplyr all 2.4.0+dfsg-1 [1172 kB]
191s Get:314 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-filelock arm64 1.0.3-1 [29.7 kB]
191s Get:315 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biocfilecache all 2.12.0+dfsg-1 [304 kB]
191s Get:316 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biocio all 1.14.0+dfsg-1 [215 kB]
191s Get:317 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-formatr all 1.14-2 [152 kB]
191s Get:318 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lambda.r all 1.2.4-2build1 [119 kB]
191s Get:319 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-futile.options all 1.0.1-3build1 [20.2 kB]
191s Get:320 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-futile.logger all 1.4.3-4build1 [99.3 kB]
191s Get:321 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-snow all 1:0.4.4-2 [97.6 kB]
191s Get:322 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-codetools all 0.2-20-1 [90.5 kB]
191s Get:323 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bh all 1.84.0-1 [5962 B]
191s Get:324 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biocparallel arm64 1.38.0-2 [1332 kB]
191s Get:325 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-base64enc arm64 0.1-3-3 [27.4 kB]
191s Get:326 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-digest arm64 0.6.36-1 [197 kB]
191s Get:327 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-htmltools arm64 0.5.8.1-1 [373 kB]
191s Get:328 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-evaluate all 0.24.0-1 [93.5 kB]
191s Get:329 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-xfun arm64 0.45+dfsg-1 [517 kB]
191s Get:330 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-highr all 0.11+dfsg-1 [38.5 kB]
191s Get:331 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-yaml arm64 2.3.8-2 [108 kB]
191s Get:332 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
191s Get:333 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-knitr all 1.47+dfsg-1 [911 kB]
191s Get:334 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.5 kB]
191s Get:335 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fs arm64 1.6.4+dfsg-1 [244 kB]
191s Get:336 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rappdirs arm64 0.3.3-1 [47.5 kB]
191s Get:337 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-sass arm64 0.4.9+dfsg-1 [957 kB]
191s Get:338 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bslib all 0.7.0+dfsg-1 [4255 kB]
191s Get:339 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fontawesome all 0.5.2-1 [1300 kB]
191s Get:340 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tinytex all 0.51-1 [145 kB]
191s Get:341 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-modernizr all 3.13.0-0.1 [101 kB]
191s Get:342 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB]
191s Get:343 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcpp arm64 1.0.13-1 [1981 kB]
192s Get:344 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-later arm64 1.3.2+dfsg-1 [120 kB]
192s Get:345 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-promises arm64 1.3.0+dfsg-1 [286 kB]
192s Get:346 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-httpuv arm64 1.6.15+dfsg-1 [489 kB]
192s Get:347 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-sourcetools arm64 0.1.7-1-1 [47.2 kB]
192s Get:348 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-commonmark arm64 1.9.1-1 [127 kB]
192s Get:349 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB]
192s Get:350 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-shiny all 1.8.1.1+dfsg-1 [2873 kB]
192s Get:351 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rmarkdown all 2.27+dfsg-1 [1501 kB]
192s Get:352 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bookdown all 0.40+dfsg-1 [1409 kB]
192s Get:353 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-biocmanager all 1.30.22+dfsg-2 [125 kB]
192s Get:354 http://ftpmaster.internal/ubuntu plucky/universe arm64 tex-common all 6.18 [32.8 kB]
192s Get:355 http://ftpmaster.internal/ubuntu plucky/main arm64 t1utils arm64 1.41-4build3 [61.0 kB]
192s Get:356 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-binaries arm64 2024.20240313.70630+ds-4 [8319 kB]
192s Get:357 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-base all 2024.20240706-1 [22.5 MB]
193s Get:358 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-latex-base all 2024.20240706-1 [1256 kB]
193s Get:359 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-bibtex-extra all 2024.20240706-2 [79.1 MB]
198s Get:360 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biocversion all 3.19.1-1 [11.2 kB]
198s Get:361 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biocstyle all 2.32.1+dfsg-1 [452 kB]
198s Get:362 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-hms all 1.1.3-1 [96.5 kB]
198s Get:363 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-prettyunits all 1.2.0-1 [162 kB]
198s Get:364 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-progress all 1.2.3-1 [91.9 kB]
198s Get:365 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-httr2 all 1.0.2-1 [571 kB]
198s Get:366 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-xml2 arm64 1.3.6-1 [321 kB]
198s Get:367 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biomart all 2.60.1+dfsg-1 [431 kB]
198s Get:368 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB]
198s Get:369 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrix arm64 1.7-0-3 [4109 kB]
198s Get:370 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrixstats arm64 1.3.0-1 [493 kB]
198s Get:371 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-matrixgenerics all 1.16.0-2 [424 kB]
198s Get:372 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-abind all 1.4-5-2 [63.6 kB]
198s Get:373 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-s4arrays arm64 1.4.1+dfsg-1 [521 kB]
198s Get:374 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-sparsearray arm64 1.4.8+dfsg-1 [1252 kB]
199s Get:375 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-delayedarray arm64 0.30.1+dfsg-1 [1839 kB]
199s Get:376 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-genomicranges arm64 1.56.1+dfsg-1 [1837 kB]
199s Get:377 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-summarizedexperiment all 1.34.0+dfsg-1 [1134 kB]
199s Get:378 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-locfit arm64 1.5-9.9-1 [514 kB]
199s Get:379 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-gtable all 0.3.5+dfsg-1 [192 kB]
199s Get:380 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB]
199s Get:381 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mass arm64 7.3-61-1 [1107 kB]
199s Get:382 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nlme arm64 3.1.166-1 [2312 kB]
199s Get:383 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB]
199s Get:384 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-farver arm64 2.1.2-1 [1344 kB]
199s Get:385 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB]
199s Get:386 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-colorspace arm64 2.1-0+dfsg-1 [1540 kB]
199s Get:387 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-munsell all 0.5.1-1 [213 kB]
199s Get:388 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB]
199s Get:389 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB]
199s Get:390 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-scales all 1.3.0-1 [603 kB]
199s Get:391 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB]
200s Get:392 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcpparmadillo arm64 14.0.0-1-1 [863 kB]
200s Get:393 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-deseq2 arm64 1.44.0+dfsg-1 [1234 kB]
200s Get:394 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-hwriter all 1.3.2.1-1 [106 kB]
200s Get:395 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bitops arm64 1.0-7-1 [29.5 kB]
200s Get:396 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-rhtslib arm64 3.0.0+dfsg-1 [1427 kB]
200s Get:397 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-rsamtools arm64 2.20.0+dfsg-1 [3668 kB]
200s Get:398 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-statmod arm64 1.5.0-1 [294 kB]
200s Get:399 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-geneplotter all 1.82.0+dfsg-1 [1417 kB]
200s Get:400 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-survival arm64 3.7-0-1 [6268 kB]
200s Get:401 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-genefilter arm64 1.86.0-1 [1116 kB]
200s Get:402 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-dexseq all 1.50.0+dfsg-1 [452 kB]
200s Get:403 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-limma arm64 3.60.4+dfsg-1 [1952 kB]
201s Get:404 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-edger arm64 4.2.1+dfsg-1 [1170 kB]
201s Get:405 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-genomicalignments arm64 1.40.0-1 [2164 kB]
201s Get:406 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcurl arm64 1.98-1.14+dfsg-1build2 [793 kB]
201s Get:407 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rjson arm64 0.2.21-1 [142 kB]
201s Get:408 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-restfulr arm64 0.0.15-1 [380 kB]
201s Get:409 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-rtracklayer arm64 1.64.0-1 [5068 kB]
202s Get:410 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-genomicfeatures all 1.56.0+dfsg-1 [980 kB]
203s Get:411 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-txdbmaker all 1.0.1+ds-1 [875 kB]
203s Get:412 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-genelendatabase all 1.40.1-1 [100 MB]
208s Get:413 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-go.db all 3.19.1-1 [17.7 MB]
208s Get:414 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-biasedurn arm64 2.0.11-1 [276 kB]
208s Get:415 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-goseq all 1.56.0-1 [1754 kB]
209s Get:416 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-plyr arm64 1.8.9-1 [831 kB]
209s Get:417 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-reshape2 arm64 1.4.4-2build1 [110 kB]
209s Get:418 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-qvalue all 2.36.0-1 [2805 kB]
209s Get:419 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-findpython all 1.0.8-1 [24.2 kB]
209s Get:420 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-argparse all 2.2.3+dfsg-1 [143 kB]
209s Get:421 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-backports arm64 1.5.0-2 [121 kB]
209s Get:422 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-broom all 1.0.6+dfsg-1 [1803 kB]
209s Get:423 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ps arm64 1.7.6-1 [313 kB]
209s Get:424 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-processx arm64 3.8.4-1 [352 kB]
209s Get:425 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-callr all 3.7.6-1 [458 kB]
209s Get:426 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rematch all 2.0.0-1 [18.3 kB]
209s Get:427 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cellranger all 1.1.0-3 [102 kB]
209s Get:428 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-clipr all 0.8.0-1 [53.5 kB]
209s Get:429 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cluster arm64 2.1.6-1build1 [551 kB]
209s Get:430 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-conflicted all 1.2.0-1.1 [60.8 kB]
209s Get:431 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-data.table arm64 1.15.4+dfsg-2.2 [1858 kB]
209s Get:432 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-dtplyr all 1.3.1-1 [364 kB]
209s Get:433 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ellipsis arm64 0.3.2-2 [35.5 kB]
209s Get:434 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fastcluster arm64 1.2.6-1build1 [190 kB]
209s Get:435 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-forcats all 1.0.0-1 [369 kB]
209s Get:436 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-gargle all 1.5.2-1 [737 kB]
209s Get:437 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ggdendro all 0.2.0+dfsg-1 [173 kB]
209s Get:438 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-uuid arm64 1.2-1-1 [48.7 kB]
209s Get:439 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-googledrive all 2.1.1-1 [1224 kB]
209s Get:440 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ids all 1.0.1-2 [124 kB]
209s Get:441 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rematch2 all 2.1.2-2build1 [46.5 kB]
209s Get:442 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-googlesheets4 all 1.1.1-1 [520 kB]
209s Get:443 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-gridextra all 2.3-3build1 [1024 kB]
209s Get:444 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-goplot all 1.0.2-2 [2427 kB]
209s Get:445 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tzdb arm64 0.4.0-2 [512 kB]
209s Get:446 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-vroom arm64 1.6.5-1 [832 kB]
209s Get:447 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-readr arm64 2.1.5-1 [756 kB]
209s Get:448 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-haven arm64 2.5.4-1 [338 kB]
209s Get:449 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-kernsmooth arm64 2.23-24-1 [92.6 kB]
209s Get:450 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-timechange arm64 0.3.0-1 [172 kB]
209s Get:451 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lubridate arm64 1.9.3+dfsg-1 [1010 kB]
210s Get:452 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-modelr all 0.1.11-1 [195 kB]
210s Get:453 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-systemfonts arm64 1.1.0-1 [236 kB]
210s Get:454 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-textshaping arm64 0.3.7-2 [91.8 kB]
210s Get:455 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ragg arm64 1.3.2-1 [477 kB]
210s Get:456 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-readxl arm64 1.4.3-1 [726 kB]
210s Get:457 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rstudioapi all 0.16.0-1 [287 kB]
210s Get:458 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-reprex all 2.1.0-1 [465 kB]
210s Get:459 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-selectr all 0.4-2-2build1 [416 kB]
210s Get:460 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rvest all 1.0.4-1 [298 kB]
210s Get:461 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tidyverse all 2.0.0+dfsg-1 [84.5 kB]
210s Get:462 http://ftpmaster.internal/ubuntu plucky/universe arm64 bowtie arm64 1.3.1-3 [1346 kB]
210s Get:463 http://ftpmaster.internal/ubuntu plucky/universe arm64 bowtie2 arm64 2.5.4-1 [1380 kB]
210s Get:464 http://ftpmaster.internal/ubuntu plucky/universe arm64 rsem arm64 1.3.3+dfsg-3build1 [36.0 MB]
211s Get:465 http://ftpmaster.internal/ubuntu plucky/universe arm64 salmon arm64 1.10.2+ds1-1build2 [3239 kB]
212s Get:466 http://ftpmaster.internal/ubuntu plucky/universe arm64 samtools arm64 1.20-3 [590 kB]
212s Get:467 http://ftpmaster.internal/ubuntu plucky/universe arm64 subread arm64 2.0.6+dfsg-3 [598 kB]
212s Get:468 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjbzip2-java all 0.9.1-8 [42.4 kB]
212s Get:469 http://ftpmaster.internal/ubuntu plucky/universe arm64 trimmomatic all 0.39+dfsg-2 [758 kB]
212s Get:470 http://ftpmaster.internal/ubuntu plucky/universe arm64 trinityrnaseq arm64 2.15.1+dfsg-5build1 [1730 kB]
212s Get:471 http://ftpmaster.internal/ubuntu plucky/universe arm64 trinityrnaseq-examples arm64 2.15.1+dfsg-5build1 [299 MB]
225s Preconfiguring packages ...
226s Fetched 983 MB in 49s (20.2 MB/s)
226s Selecting previously unselected package libgdk-pixbuf2.0-common.
226s (Reading database ... 
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226s Preparing to unpack .../000-libgdk-pixbuf2.0-common_2.42.12+dfsg-1_all.deb ...
226s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ...
226s Selecting previously unselected package libjpeg-turbo8:arm64.
226s Preparing to unpack .../001-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ...
226s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ...
226s Selecting previously unselected package libjpeg8:arm64.
226s Preparing to unpack .../002-libjpeg8_8c-2ubuntu11_arm64.deb ...
226s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
226s Selecting previously unselected package libdeflate0:arm64.
226s Preparing to unpack .../003-libdeflate0_1.21-1_arm64.deb ...
226s Unpacking libdeflate0:arm64 (1.21-1) ...
226s Selecting previously unselected package libjbig0:arm64.
226s Preparing to unpack .../004-libjbig0_2.1-6.1ubuntu2_arm64.deb ...
226s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ...
226s Selecting previously unselected package liblerc4:arm64.
226s Preparing to unpack .../005-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ...
226s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ...
226s Selecting previously unselected package libsharpyuv0:arm64.
226s Preparing to unpack .../006-libsharpyuv0_1.4.0-0.1_arm64.deb ...
226s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ...
226s Selecting previously unselected package libwebp7:arm64.
226s Preparing to unpack .../007-libwebp7_1.4.0-0.1_arm64.deb ...
226s Unpacking libwebp7:arm64 (1.4.0-0.1) ...
226s Selecting previously unselected package libtiff6:arm64.
226s Preparing to unpack .../008-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ...
226s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
226s Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64.
226s Preparing to unpack .../009-libgdk-pixbuf-2.0-0_2.42.12+dfsg-1_arm64.deb ...
226s Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-1) ...
226s Selecting previously unselected package gtk-update-icon-cache.
226s Preparing to unpack .../010-gtk-update-icon-cache_4.16.2+ds-2_arm64.deb ...
226s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed.
226s 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.
226s Unpacking gtk-update-icon-cache (4.16.2+ds-2) ...
226s Selecting previously unselected package hicolor-icon-theme.
226s Preparing to unpack .../011-hicolor-icon-theme_0.18-1_all.deb ...
226s Unpacking hicolor-icon-theme (0.18-1) ...
227s Selecting previously unselected package humanity-icon-theme.
227s Preparing to unpack .../012-humanity-icon-theme_0.6.16_all.deb ...
227s Unpacking humanity-icon-theme (0.6.16) ...
227s Selecting previously unselected package ubuntu-mono.
227s Preparing to unpack .../013-ubuntu-mono_24.04-0ubuntu1_all.deb ...
227s Unpacking ubuntu-mono (24.04-0ubuntu1) ...
227s Selecting previously unselected package adwaita-icon-theme.
227s Preparing to unpack .../014-adwaita-icon-theme_47.0-1_all.deb ...
227s Unpacking adwaita-icon-theme (47.0-1) ...
228s Selecting previously unselected package at-spi2-common.
228s Preparing to unpack .../015-at-spi2-common_2.54.0-1_all.deb ...
228s Unpacking at-spi2-common (2.54.0-1) ...
228s Selecting previously unselected package libbamtools2.5.2:arm64.
228s Preparing to unpack .../016-libbamtools2.5.2_2.5.2+dfsg-6_arm64.deb ...
228s Unpacking libbamtools2.5.2:arm64 (2.5.2+dfsg-6) ...
228s Selecting previously unselected package libboost-filesystem1.83.0:arm64.
228s Preparing to unpack .../017-libboost-filesystem1.83.0_1.83.0-3.2ubuntu2_arm64.deb ...
228s Unpacking libboost-filesystem1.83.0:arm64 (1.83.0-3.2ubuntu2) ...
228s Selecting previously unselected package libboost-program-options1.83.0:arm64.
228s Preparing to unpack .../018-libboost-program-options1.83.0_1.83.0-3.2ubuntu2_arm64.deb ...
228s Unpacking libboost-program-options1.83.0:arm64 (1.83.0-3.2ubuntu2) ...
228s Selecting previously unselected package libboost-thread1.83.0:arm64.
228s Preparing to unpack .../019-libboost-thread1.83.0_1.83.0-3.2ubuntu2_arm64.deb ...
228s Unpacking libboost-thread1.83.0:arm64 (1.83.0-3.2ubuntu2) ...
228s Selecting previously unselected package libprotobuf32t64:arm64.
228s Preparing to unpack .../020-libprotobuf32t64_3.21.12-9ubuntu1_arm64.deb ...
228s Unpacking libprotobuf32t64:arm64 (3.21.12-9ubuntu1) ...
228s Selecting previously unselected package berkeley-express.
228s Preparing to unpack .../021-berkeley-express_1.5.3+dfsg-3build5_arm64.deb ...
228s Unpacking berkeley-express (1.5.3+dfsg-3build5) ...
228s Selecting previously unselected package ca-certificates-java.
228s Preparing to unpack .../022-ca-certificates-java_20240118_all.deb ...
228s Unpacking ca-certificates-java (20240118) ...
228s Selecting previously unselected package libdconf1:arm64.
228s Preparing to unpack .../023-libdconf1_0.40.0-4build2_arm64.deb ...
228s Unpacking libdconf1:arm64 (0.40.0-4build2) ...
228s Selecting previously unselected package dconf-service.
228s Preparing to unpack .../024-dconf-service_0.40.0-4build2_arm64.deb ...
228s Unpacking dconf-service (0.40.0-4build2) ...
228s Selecting previously unselected package dconf-gsettings-backend:arm64.
228s Preparing to unpack .../025-dconf-gsettings-backend_0.40.0-4build2_arm64.deb ...
228s Unpacking dconf-gsettings-backend:arm64 (0.40.0-4build2) ...
228s Selecting previously unselected package java-common.
228s Preparing to unpack .../026-java-common_0.76_all.deb ...
228s Unpacking java-common (0.76) ...
228s Selecting previously unselected package liblcms2-2:arm64.
228s Preparing to unpack .../027-liblcms2-2_2.14-2build1_arm64.deb ...
228s Unpacking liblcms2-2:arm64 (2.14-2build1) ...
228s Selecting previously unselected package libpcsclite1:arm64.
228s Preparing to unpack .../028-libpcsclite1_2.3.0-1_arm64.deb ...
228s Unpacking libpcsclite1:arm64 (2.3.0-1) ...
228s Selecting previously unselected package openjdk-21-jre-headless:arm64.
228s Preparing to unpack .../029-openjdk-21-jre-headless_21.0.5+11-1_arm64.deb ...
228s Unpacking openjdk-21-jre-headless:arm64 (21.0.5+11-1) ...
229s Selecting previously unselected package default-jre-headless.
230s Preparing to unpack .../030-default-jre-headless_2%3a1.21-76_arm64.deb ...
230s Unpacking default-jre-headless (2:1.21-76) ...
230s Selecting previously unselected package libatk1.0-0t64:arm64.
230s Preparing to unpack .../031-libatk1.0-0t64_2.54.0-1_arm64.deb ...
230s Unpacking libatk1.0-0t64:arm64 (2.54.0-1) ...
230s Selecting previously unselected package libxi6:arm64.
230s Preparing to unpack .../032-libxi6_2%3a1.8.2-1_arm64.deb ...
230s Unpacking libxi6:arm64 (2:1.8.2-1) ...
230s Selecting previously unselected package libatspi2.0-0t64:arm64.
230s Preparing to unpack .../033-libatspi2.0-0t64_2.54.0-1_arm64.deb ...
230s Unpacking libatspi2.0-0t64:arm64 (2.54.0-1) ...
230s Selecting previously unselected package libatk-bridge2.0-0t64:arm64.
230s Preparing to unpack .../034-libatk-bridge2.0-0t64_2.54.0-1_arm64.deb ...
230s Unpacking libatk-bridge2.0-0t64:arm64 (2.54.0-1) ...
230s Selecting previously unselected package fonts-dejavu-mono.
230s Preparing to unpack .../035-fonts-dejavu-mono_2.37-8_all.deb ...
230s Unpacking fonts-dejavu-mono (2.37-8) ...
230s Selecting previously unselected package fonts-dejavu-core.
230s Preparing to unpack .../036-fonts-dejavu-core_2.37-8_all.deb ...
230s Unpacking fonts-dejavu-core (2.37-8) ...
230s Selecting previously unselected package fontconfig-config.
230s Preparing to unpack .../037-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ...
230s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
230s Selecting previously unselected package libfontconfig1:arm64.
230s Preparing to unpack .../038-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ...
230s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ...
230s Selecting previously unselected package libpixman-1-0:arm64.
230s Preparing to unpack .../039-libpixman-1-0_0.42.2-1build1_arm64.deb ...
230s Unpacking libpixman-1-0:arm64 (0.42.2-1build1) ...
230s Selecting previously unselected package libxcb-render0:arm64.
230s Preparing to unpack .../040-libxcb-render0_1.17.0-2_arm64.deb ...
230s Unpacking libxcb-render0:arm64 (1.17.0-2) ...
230s Selecting previously unselected package libxcb-shm0:arm64.
230s Preparing to unpack .../041-libxcb-shm0_1.17.0-2_arm64.deb ...
230s Unpacking libxcb-shm0:arm64 (1.17.0-2) ...
230s Selecting previously unselected package libxrender1:arm64.
230s Preparing to unpack .../042-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ...
230s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ...
230s Selecting previously unselected package libcairo2:arm64.
230s Preparing to unpack .../043-libcairo2_1.18.2-2_arm64.deb ...
230s Unpacking libcairo2:arm64 (1.18.2-2) ...
230s Selecting previously unselected package libcairo-gobject2:arm64.
230s Preparing to unpack .../044-libcairo-gobject2_1.18.2-2_arm64.deb ...
230s Unpacking libcairo-gobject2:arm64 (1.18.2-2) ...
230s Selecting previously unselected package libcolord2:arm64.
230s Preparing to unpack .../045-libcolord2_1.4.7-1build2_arm64.deb ...
230s Unpacking libcolord2:arm64 (1.4.7-1build2) ...
231s Selecting previously unselected package libavahi-common-data:arm64.
231s Preparing to unpack .../046-libavahi-common-data_0.8-13ubuntu6_arm64.deb ...
231s Unpacking libavahi-common-data:arm64 (0.8-13ubuntu6) ...
231s Selecting previously unselected package libavahi-common3:arm64.
231s Preparing to unpack .../047-libavahi-common3_0.8-13ubuntu6_arm64.deb ...
231s Unpacking libavahi-common3:arm64 (0.8-13ubuntu6) ...
231s Selecting previously unselected package libavahi-client3:arm64.
231s Preparing to unpack .../048-libavahi-client3_0.8-13ubuntu6_arm64.deb ...
231s Unpacking libavahi-client3:arm64 (0.8-13ubuntu6) ...
231s Selecting previously unselected package libcups2t64:arm64.
231s Preparing to unpack .../049-libcups2t64_2.4.10-1ubuntu2_arm64.deb ...
231s Unpacking libcups2t64:arm64 (2.4.10-1ubuntu2) ...
231s Selecting previously unselected package libepoxy0:arm64.
231s Preparing to unpack .../050-libepoxy0_1.5.10-1build1_arm64.deb ...
231s Unpacking libepoxy0:arm64 (1.5.10-1build1) ...
231s Selecting previously unselected package libgraphite2-3:arm64.
231s Preparing to unpack .../051-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ...
231s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
231s Selecting previously unselected package libharfbuzz0b:arm64.
231s Preparing to unpack .../052-libharfbuzz0b_9.0.0-1_arm64.deb ...
231s Unpacking libharfbuzz0b:arm64 (9.0.0-1) ...
231s Selecting previously unselected package fontconfig.
231s Preparing to unpack .../053-fontconfig_2.15.0-1.1ubuntu2_arm64.deb ...
231s Unpacking fontconfig (2.15.0-1.1ubuntu2) ...
231s Selecting previously unselected package libthai-data.
231s Preparing to unpack .../054-libthai-data_0.1.29-2build1_all.deb ...
231s Unpacking libthai-data (0.1.29-2build1) ...
231s Selecting previously unselected package libdatrie1:arm64.
231s Preparing to unpack .../055-libdatrie1_0.2.13-3build1_arm64.deb ...
231s Unpacking libdatrie1:arm64 (0.2.13-3build1) ...
231s Selecting previously unselected package libthai0:arm64.
231s Preparing to unpack .../056-libthai0_0.1.29-2build1_arm64.deb ...
231s Unpacking libthai0:arm64 (0.1.29-2build1) ...
231s Selecting previously unselected package libpango-1.0-0:arm64.
231s Preparing to unpack .../057-libpango-1.0-0_1.54.0+ds-2_arm64.deb ...
231s Unpacking libpango-1.0-0:arm64 (1.54.0+ds-2) ...
231s Selecting previously unselected package libpangoft2-1.0-0:arm64.
231s Preparing to unpack .../058-libpangoft2-1.0-0_1.54.0+ds-2_arm64.deb ...
231s Unpacking libpangoft2-1.0-0:arm64 (1.54.0+ds-2) ...
231s Selecting previously unselected package libpangocairo-1.0-0:arm64.
231s Preparing to unpack .../059-libpangocairo-1.0-0_1.54.0+ds-2_arm64.deb ...
231s Unpacking libpangocairo-1.0-0:arm64 (1.54.0+ds-2) ...
231s Selecting previously unselected package libwayland-client0:arm64.
231s Preparing to unpack .../060-libwayland-client0_1.23.0-1_arm64.deb ...
231s Unpacking libwayland-client0:arm64 (1.23.0-1) ...
231s Selecting previously unselected package libwayland-cursor0:arm64.
231s Preparing to unpack .../061-libwayland-cursor0_1.23.0-1_arm64.deb ...
231s Unpacking libwayland-cursor0:arm64 (1.23.0-1) ...
231s Selecting previously unselected package libwayland-egl1:arm64.
231s Preparing to unpack .../062-libwayland-egl1_1.23.0-1_arm64.deb ...
231s Unpacking libwayland-egl1:arm64 (1.23.0-1) ...
231s Selecting previously unselected package libxcomposite1:arm64.
231s Preparing to unpack .../063-libxcomposite1_1%3a0.4.5-1build3_arm64.deb ...
231s Unpacking libxcomposite1:arm64 (1:0.4.5-1build3) ...
231s Selecting previously unselected package libxfixes3:arm64.
231s Preparing to unpack .../064-libxfixes3_1%3a6.0.0-2build1_arm64.deb ...
231s Unpacking libxfixes3:arm64 (1:6.0.0-2build1) ...
231s Selecting previously unselected package libxcursor1:arm64.
231s Preparing to unpack .../065-libxcursor1_1%3a1.2.2-1_arm64.deb ...
231s Unpacking libxcursor1:arm64 (1:1.2.2-1) ...
232s Selecting previously unselected package libxdamage1:arm64.
232s Preparing to unpack .../066-libxdamage1_1%3a1.1.6-1build1_arm64.deb ...
232s Unpacking libxdamage1:arm64 (1:1.1.6-1build1) ...
232s Selecting previously unselected package libxinerama1:arm64.
232s Preparing to unpack .../067-libxinerama1_2%3a1.1.4-3build1_arm64.deb ...
232s Unpacking libxinerama1:arm64 (2:1.1.4-3build1) ...
232s Selecting previously unselected package libxrandr2:arm64.
232s Preparing to unpack .../068-libxrandr2_2%3a1.5.4-1_arm64.deb ...
232s Unpacking libxrandr2:arm64 (2:1.5.4-1) ...
232s Selecting previously unselected package libgtk-3-common.
232s Preparing to unpack .../069-libgtk-3-common_3.24.43-3ubuntu2_all.deb ...
232s Unpacking libgtk-3-common (3.24.43-3ubuntu2) ...
232s Selecting previously unselected package libgtk-3-0t64:arm64.
232s Preparing to unpack .../070-libgtk-3-0t64_3.24.43-3ubuntu2_arm64.deb ...
232s Unpacking libgtk-3-0t64:arm64 (3.24.43-3ubuntu2) ...
232s Selecting previously unselected package libglvnd0:arm64.
232s Preparing to unpack .../071-libglvnd0_1.7.0-1build1_arm64.deb ...
232s Unpacking libglvnd0:arm64 (1.7.0-1build1) ...
232s Selecting previously unselected package libglapi-mesa:arm64.
232s Preparing to unpack .../072-libglapi-mesa_24.2.3-1ubuntu1_arm64.deb ...
232s Unpacking libglapi-mesa:arm64 (24.2.3-1ubuntu1) ...
232s Selecting previously unselected package libx11-xcb1:arm64.
232s Preparing to unpack .../073-libx11-xcb1_2%3a1.8.7-1build1_arm64.deb ...
232s Unpacking libx11-xcb1:arm64 (2:1.8.7-1build1) ...
232s Selecting previously unselected package libxcb-dri2-0:arm64.
232s Preparing to unpack .../074-libxcb-dri2-0_1.17.0-2_arm64.deb ...
232s Unpacking libxcb-dri2-0:arm64 (1.17.0-2) ...
232s Selecting previously unselected package libxcb-dri3-0:arm64.
232s Preparing to unpack .../075-libxcb-dri3-0_1.17.0-2_arm64.deb ...
232s Unpacking libxcb-dri3-0:arm64 (1.17.0-2) ...
232s Selecting previously unselected package libxcb-glx0:arm64.
232s Preparing to unpack .../076-libxcb-glx0_1.17.0-2_arm64.deb ...
232s Unpacking libxcb-glx0:arm64 (1.17.0-2) ...
232s Selecting previously unselected package libxcb-present0:arm64.
232s Preparing to unpack .../077-libxcb-present0_1.17.0-2_arm64.deb ...
232s Unpacking libxcb-present0:arm64 (1.17.0-2) ...
232s Selecting previously unselected package libxcb-randr0:arm64.
232s Preparing to unpack .../078-libxcb-randr0_1.17.0-2_arm64.deb ...
232s Unpacking libxcb-randr0:arm64 (1.17.0-2) ...
232s Selecting previously unselected package libxcb-sync1:arm64.
232s Preparing to unpack .../079-libxcb-sync1_1.17.0-2_arm64.deb ...
232s Unpacking libxcb-sync1:arm64 (1.17.0-2) ...
232s Selecting previously unselected package libxcb-xfixes0:arm64.
232s Preparing to unpack .../080-libxcb-xfixes0_1.17.0-2_arm64.deb ...
232s Unpacking libxcb-xfixes0:arm64 (1.17.0-2) ...
232s Selecting previously unselected package libxshmfence1:arm64.
232s Preparing to unpack .../081-libxshmfence1_1.3-1build5_arm64.deb ...
232s Unpacking libxshmfence1:arm64 (1.3-1build5) ...
232s Selecting previously unselected package libxxf86vm1:arm64.
232s Preparing to unpack .../082-libxxf86vm1_1%3a1.1.4-1build4_arm64.deb ...
232s Unpacking libxxf86vm1:arm64 (1:1.1.4-1build4) ...
232s Selecting previously unselected package libdrm-amdgpu1:arm64.
232s Preparing to unpack .../083-libdrm-amdgpu1_2.4.122-1_arm64.deb ...
232s Unpacking libdrm-amdgpu1:arm64 (2.4.122-1) ...
233s Selecting previously unselected package libdrm-radeon1:arm64.
233s Preparing to unpack .../084-libdrm-radeon1_2.4.122-1_arm64.deb ...
233s Unpacking libdrm-radeon1:arm64 (2.4.122-1) ...
233s Selecting previously unselected package mesa-libgallium:arm64.
233s Preparing to unpack .../085-mesa-libgallium_24.2.3-1ubuntu1_arm64.deb ...
233s Unpacking mesa-libgallium:arm64 (24.2.3-1ubuntu1) ...
233s Selecting previously unselected package libvulkan1:arm64.
233s Preparing to unpack .../086-libvulkan1_1.3.290.0-1_arm64.deb ...
233s Unpacking libvulkan1:arm64 (1.3.290.0-1) ...
233s Selecting previously unselected package libwayland-server0:arm64.
233s Preparing to unpack .../087-libwayland-server0_1.23.0-1_arm64.deb ...
233s Unpacking libwayland-server0:arm64 (1.23.0-1) ...
233s Selecting previously unselected package libgbm1:arm64.
233s Preparing to unpack .../088-libgbm1_24.2.3-1ubuntu1_arm64.deb ...
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233s Selecting previously unselected package libgl1-mesa-dri:arm64.
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233s Selecting previously unselected package libglx-mesa0:arm64.
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233s Selecting previously unselected package libglx0:arm64.
233s Preparing to unpack .../091-libglx0_1.7.0-1build1_arm64.deb ...
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233s Selecting previously unselected package libgl1:arm64.
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233s Selecting previously unselected package libasound2-data.
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233s Selecting previously unselected package libasound2t64:arm64.
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233s Selecting previously unselected package libgif7:arm64.
233s Preparing to unpack .../095-libgif7_5.2.2-1ubuntu1_arm64.deb ...
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233s Selecting previously unselected package x11-common.
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233s Selecting previously unselected package libxtst6:arm64.
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233s Selecting previously unselected package openjdk-21-jre:arm64.
233s Preparing to unpack .../098-openjdk-21-jre_21.0.5+11-1_arm64.deb ...
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234s Selecting previously unselected package fonts-font-awesome.
234s Preparing to unpack .../100-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ...
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234s Selecting previously unselected package fonts-glyphicons-halflings.
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234s Selecting previously unselected package fonts-lmodern.
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234s Selecting previously unselected package fonts-mathjax.
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234s Selecting previously unselected package hisat2.
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234s Selecting previously unselected package jaligner.
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234s Selecting previously unselected package javascript-common.
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234s Selecting previously unselected package libhtscodecs2:arm64.
234s Preparing to unpack .../107-libhtscodecs2_1.6.0-1build1_arm64.deb ...
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234s Selecting previously unselected package libhts3t64:arm64.
234s Preparing to unpack .../108-libhts3t64_1.20+ds-1_arm64.deb ...
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234s Selecting previously unselected package libjellyfish-2.0-2:arm64.
234s Preparing to unpack .../109-libjellyfish-2.0-2_2.3.1-3build2_arm64.deb ...
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234s Selecting previously unselected package jellyfish.
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234s Unpacking jellyfish (2.3.1-3build2) ...
235s Selecting previously unselected package kallisto.
235s Preparing to unpack .../111-kallisto_0.48.0+dfsg-4build1_arm64.deb ...
235s Unpacking kallisto (0.48.0+dfsg-4build1) ...
235s Selecting previously unselected package libapache-pom-java.
235s Preparing to unpack .../112-libapache-pom-java_29-2_all.deb ...
235s Unpacking libapache-pom-java (29-2) ...
235s Selecting previously unselected package libasan8:arm64.
235s Preparing to unpack .../113-libasan8_14.2.0-7ubuntu1_arm64.deb ...
235s Unpacking libasan8:arm64 (14.2.0-7ubuntu1) ...
235s Selecting previously unselected package libatinject-jsr330-api-java.
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235s Selecting previously unselected package libcommons-parent-java.
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235s Selecting previously unselected package libcommons-lang3-java.
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235s Selecting previously unselected package libfreemarker-java.
235s Preparing to unpack .../117-libfreemarker-java_2.3.32-2_all.deb ...
235s Unpacking libfreemarker-java (2.3.32-2) ...
235s Selecting previously unselected package libgoogle-gson-java.
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235s Unpacking libgoogle-gson-java (2.10.1-1) ...
235s Selecting previously unselected package libjoptsimple-java.
235s Preparing to unpack .../119-libjoptsimple-java_5.0.4-4_all.deb ...
235s Unpacking libjoptsimple-java (5.0.4-4) ...
235s Selecting previously unselected package libcommons-codec-java.
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235s Unpacking libcommons-codec-java (1.16.0-1) ...
235s Selecting previously unselected package libcommons-logging-java.
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235s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ...
235s Selecting previously unselected package libhttpcore-java.
235s Preparing to unpack .../122-libhttpcore-java_4.4.16-1_all.deb ...
235s Unpacking libhttpcore-java (4.4.16-1) ...
235s Selecting previously unselected package libhttpclient-java.
235s Preparing to unpack .../123-libhttpclient-java_4.5.14-1_all.deb ...
235s Unpacking libhttpclient-java (4.5.14-1) ...
235s Selecting previously unselected package liblightcouch-java.
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235s Unpacking liblightcouch-java (0.2.0-1) ...
235s Selecting previously unselected package libmongodb-java.
235s Preparing to unpack .../125-libmongodb-java_3.6.3-2_all.deb ...
235s Unpacking libmongodb-java (3.6.3-2) ...
236s Selecting previously unselected package libslf4j-java.
236s Preparing to unpack .../126-libslf4j-java_1.7.32-1_all.deb ...
236s Unpacking libslf4j-java (1.7.32-1) ...
236s Selecting previously unselected package liblog4j2-java.
236s Preparing to unpack .../127-liblog4j2-java_2.19.0-2_all.deb ...
236s Unpacking liblog4j2-java (2.19.0-2) ...
236s Selecting previously unselected package libbarclay-java.
236s Preparing to unpack .../128-libbarclay-java_5.0.0+dfsg-1_all.deb ...
236s Unpacking libbarclay-java (5.0.0+dfsg-1) ...
236s Selecting previously unselected package libio-string-perl.
236s Preparing to unpack .../129-libio-string-perl_1.08-4_all.deb ...
236s Unpacking libio-string-perl (1.08-4) ...
236s Selecting previously unselected package liblatex-tounicode-perl.
236s Preparing to unpack .../130-liblatex-tounicode-perl_0.54-2_all.deb ...
236s Unpacking liblatex-tounicode-perl (0.54-2) ...
236s Selecting previously unselected package libbibtex-parser-perl.
236s Preparing to unpack .../131-libbibtex-parser-perl_1.04+dfsg-1_all.deb ...
236s Unpacking libbibtex-parser-perl (1.04+dfsg-1) ...
236s Selecting previously unselected package libblas3:arm64.
236s Preparing to unpack .../132-libblas3_3.12.0-3build2_arm64.deb ...
236s Unpacking libblas3:arm64 (3.12.0-3build2) ...
236s Selecting previously unselected package libgomp1:arm64.
236s Preparing to unpack .../133-libgomp1_14.2.0-7ubuntu1_arm64.deb ...
236s Unpacking libgomp1:arm64 (14.2.0-7ubuntu1) ...
236s Selecting previously unselected package libitm1:arm64.
236s Preparing to unpack .../134-libitm1_14.2.0-7ubuntu1_arm64.deb ...
236s Unpacking libitm1:arm64 (14.2.0-7ubuntu1) ...
236s Selecting previously unselected package liblsan0:arm64.
236s Preparing to unpack .../135-liblsan0_14.2.0-7ubuntu1_arm64.deb ...
236s Unpacking liblsan0:arm64 (14.2.0-7ubuntu1) ...
236s Selecting previously unselected package libtsan2:arm64.
236s Preparing to unpack .../136-libtsan2_14.2.0-7ubuntu1_arm64.deb ...
236s Unpacking libtsan2:arm64 (14.2.0-7ubuntu1) ...
236s Selecting previously unselected package libubsan1:arm64.
236s Preparing to unpack .../137-libubsan1_14.2.0-7ubuntu1_arm64.deb ...
236s Unpacking libubsan1:arm64 (14.2.0-7ubuntu1) ...
236s Selecting previously unselected package libhwasan0:arm64.
236s Preparing to unpack .../138-libhwasan0_14.2.0-7ubuntu1_arm64.deb ...
236s Unpacking libhwasan0:arm64 (14.2.0-7ubuntu1) ...
236s Selecting previously unselected package libgcc-14-dev:arm64.
236s Preparing to unpack .../139-libgcc-14-dev_14.2.0-7ubuntu1_arm64.deb ...
236s Unpacking libgcc-14-dev:arm64 (14.2.0-7ubuntu1) ...
236s Selecting previously unselected package libstdc++-14-dev:arm64.
237s Preparing to unpack .../140-libstdc++-14-dev_14.2.0-7ubuntu1_arm64.deb ...
237s Unpacking libstdc++-14-dev:arm64 (14.2.0-7ubuntu1) ...
237s Selecting previously unselected package libboost1.83-dev:arm64.
237s Preparing to unpack .../141-libboost1.83-dev_1.83.0-3.2ubuntu2_arm64.deb ...
237s Unpacking libboost1.83-dev:arm64 (1.83.0-3.2ubuntu2) ...
239s Selecting previously unselected package libboost-dev:arm64.
239s Preparing to unpack .../142-libboost-dev_1.83.0.2ubuntu1_arm64.deb ...
239s Unpacking libboost-dev:arm64 (1.83.0.2ubuntu1) ...
239s Selecting previously unselected package libboost-iostreams1.83.0:arm64.
239s Preparing to unpack .../143-libboost-iostreams1.83.0_1.83.0-3.2ubuntu2_arm64.deb ...
239s Unpacking libboost-iostreams1.83.0:arm64 (1.83.0-3.2ubuntu2) ...
239s Selecting previously unselected package libclone-perl:arm64.
239s Preparing to unpack .../144-libclone-perl_0.47-1_arm64.deb ...
239s Unpacking libclone-perl:arm64 (0.47-1) ...
239s Selecting previously unselected package libcommons-compress-java.
239s Preparing to unpack .../145-libcommons-compress-java_1.25.0-1_all.deb ...
239s Unpacking libcommons-compress-java (1.25.0-1) ...
239s Selecting previously unselected package libcommons-io-java.
239s Preparing to unpack .../146-libcommons-io-java_2.16.1-1_all.deb ...
239s Unpacking libcommons-io-java (2.16.1-1) ...
239s Selecting previously unselected package libcommons-jexl2-java.
239s Preparing to unpack .../147-libcommons-jexl2-java_2.1.1-6_all.deb ...
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239s Selecting previously unselected package libcommons-math3-java.
239s Preparing to unpack .../148-libcommons-math3-java_3.6.1-3_all.deb ...
239s Unpacking libcommons-math3-java (3.6.1-3) ...
239s Selecting previously unselected package libencode-locale-perl.
239s Preparing to unpack .../149-libencode-locale-perl_1.05-3_all.deb ...
239s Unpacking libencode-locale-perl (1.05-3) ...
239s Selecting previously unselected package libjsr305-java.
239s Preparing to unpack .../150-libjsr305-java_0.1~+svn49-11_all.deb ...
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239s Selecting previously unselected package libguava-java.
239s Preparing to unpack .../151-libguava-java_32.0.1-1_all.deb ...
239s Unpacking libguava-java (32.0.1-1) ...
239s Selecting previously unselected package liberror-prone-java.
239s Preparing to unpack .../152-liberror-prone-java_2.18.0-1_all.deb ...
239s Unpacking liberror-prone-java (2.18.0-1) ...
239s Selecting previously unselected package libtimedate-perl.
239s Preparing to unpack .../153-libtimedate-perl_2.3300-2_all.deb ...
239s Unpacking libtimedate-perl (2.3300-2) ...
239s Selecting previously unselected package libhttp-date-perl.
239s Preparing to unpack .../154-libhttp-date-perl_6.06-1_all.deb ...
239s Unpacking libhttp-date-perl (6.06-1) ...
239s Selecting previously unselected package libfile-listing-perl.
239s Preparing to unpack .../155-libfile-listing-perl_6.16-1_all.deb ...
239s Unpacking libfile-listing-perl (6.16-1) ...
240s Selecting previously unselected package libgatk-native-bindings-java.
240s Preparing to unpack .../156-libgatk-native-bindings-java_1.0.0+dfsg-2_all.deb ...
240s Unpacking libgatk-native-bindings-java (1.0.0+dfsg-2) ...
240s Selecting previously unselected package libgetopt-java.
240s Preparing to unpack .../157-libgetopt-java_1.0.14+dfsg-6_all.deb ...
240s Unpacking libgetopt-java (1.0.14+dfsg-6) ...
240s Selecting previously unselected package libgfortran5:arm64.
240s Preparing to unpack .../158-libgfortran5_14.2.0-7ubuntu1_arm64.deb ...
240s Unpacking libgfortran5:arm64 (14.2.0-7ubuntu1) ...
240s Selecting previously unselected package libmjson-java.
240s Preparing to unpack .../159-libmjson-java_1.4.0-3_all.deb ...
240s Unpacking libmjson-java (1.4.0-3) ...
240s Selecting previously unselected package libmbedcrypto7t64:arm64.
240s Preparing to unpack .../160-libmbedcrypto7t64_2.28.8-1_arm64.deb ...
240s Unpacking libmbedcrypto7t64:arm64 (2.28.8-1) ...
240s Selecting previously unselected package libmbedx509-1t64:arm64.
240s Preparing to unpack .../161-libmbedx509-1t64_2.28.8-1_arm64.deb ...
240s Unpacking libmbedx509-1t64:arm64 (2.28.8-1) ...
240s Selecting previously unselected package libmbedtls14t64:arm64.
240s Preparing to unpack .../162-libmbedtls14t64_2.28.8-1_arm64.deb ...
240s Unpacking libmbedtls14t64:arm64 (2.28.8-1) ...
240s Selecting previously unselected package ncbi-vdb-data.
240s Preparing to unpack .../163-ncbi-vdb-data_3.0.2+dfsg-2build2_all.deb ...
240s Unpacking ncbi-vdb-data (3.0.2+dfsg-2build2) ...
240s Selecting previously unselected package libncbi-vdb3:arm64.
240s Preparing to unpack .../164-libncbi-vdb3_3.0.2+dfsg-2build2_arm64.deb ...
240s Unpacking libncbi-vdb3:arm64 (3.0.2+dfsg-2build2) ...
240s Selecting previously unselected package libncbi-ngs3:arm64.
240s Preparing to unpack .../165-libncbi-ngs3_3.0.3+dfsg-9ubuntu1_arm64.deb ...
240s Unpacking libncbi-ngs3:arm64 (3.0.3+dfsg-9ubuntu1) ...
240s Selecting previously unselected package libngs-jni:arm64.
240s Preparing to unpack .../166-libngs-jni_3.0.3+dfsg-9ubuntu1_arm64.deb ...
240s Unpacking libngs-jni:arm64 (3.0.3+dfsg-9ubuntu1) ...
240s Selecting previously unselected package libngs-java:arm64.
240s Preparing to unpack .../167-libngs-java_3.0.3+dfsg-9ubuntu1_arm64.deb ...
240s Unpacking libngs-java:arm64 (3.0.3+dfsg-9ubuntu1) ...
240s Selecting previously unselected package librhino-java.
240s Preparing to unpack .../168-librhino-java_1.7.14-2.1_all.deb ...
240s Unpacking librhino-java (1.7.14-2.1) ...
240s Selecting previously unselected package libsnappy1v5:arm64.
240s Preparing to unpack .../169-libsnappy1v5_1.2.1-1_arm64.deb ...
240s Unpacking libsnappy1v5:arm64 (1.2.1-1) ...
240s Selecting previously unselected package libsnappy-jni.
240s Preparing to unpack .../170-libsnappy-jni_1.1.10.5-2_arm64.deb ...
240s Unpacking libsnappy-jni (1.1.10.5-2) ...
240s Selecting previously unselected package libsnappy-java.
240s Preparing to unpack .../171-libsnappy-java_1.1.10.5-2_all.deb ...
240s Unpacking libsnappy-java (1.1.10.5-2) ...
240s Selecting previously unselected package libhtsjdk-java.
240s Preparing to unpack .../172-libhtsjdk-java_4.1.0+dfsg-2_all.deb ...
240s Unpacking libhtsjdk-java (4.1.0+dfsg-2) ...
240s Selecting previously unselected package libgkl-java.
240s Preparing to unpack .../173-libgkl-java_0.8.11+dfsg-2build1_all.deb ...
240s Unpacking libgkl-java (0.8.11+dfsg-2build1) ...
241s Selecting previously unselected package libhtml-tagset-perl.
241s Preparing to unpack .../174-libhtml-tagset-perl_3.24-1_all.deb ...
241s Unpacking libhtml-tagset-perl (3.24-1) ...
241s Selecting previously unselected package liburi-perl.
241s Preparing to unpack .../175-liburi-perl_5.30-1_all.deb ...
241s Unpacking liburi-perl (5.30-1) ...
241s Selecting previously unselected package libhtml-parser-perl:arm64.
241s Preparing to unpack .../176-libhtml-parser-perl_3.83-1build1_arm64.deb ...
241s Unpacking libhtml-parser-perl:arm64 (3.83-1build1) ...
241s Selecting previously unselected package libhtml-tree-perl.
241s Preparing to unpack .../177-libhtml-tree-perl_5.07-3_all.deb ...
241s Unpacking libhtml-tree-perl (5.07-3) ...
241s Selecting previously unselected package libio-html-perl.
241s Preparing to unpack .../178-libio-html-perl_1.004-3_all.deb ...
241s Unpacking libio-html-perl (1.004-3) ...
241s Selecting previously unselected package liblwp-mediatypes-perl.
241s Preparing to unpack .../179-liblwp-mediatypes-perl_6.04-2_all.deb ...
241s Unpacking liblwp-mediatypes-perl (6.04-2) ...
241s Selecting previously unselected package libhttp-message-perl.
241s Preparing to unpack .../180-libhttp-message-perl_6.46-1ubuntu1_all.deb ...
241s Unpacking libhttp-message-perl (6.46-1ubuntu1) ...
241s Selecting previously unselected package libhttp-cookies-perl.
241s Preparing to unpack .../181-libhttp-cookies-perl_6.11-1_all.deb ...
241s Unpacking libhttp-cookies-perl (6.11-1) ...
241s Selecting previously unselected package libhttp-negotiate-perl.
241s Preparing to unpack .../182-libhttp-negotiate-perl_6.01-2_all.deb ...
241s Unpacking libhttp-negotiate-perl (6.01-2) ...
241s Selecting previously unselected package libhwloc15:arm64.
241s Preparing to unpack .../183-libhwloc15_2.11.0-2_arm64.deb ...
241s Unpacking libhwloc15:arm64 (2.11.0-2) ...
241s Selecting previously unselected package libice6:arm64.
241s Preparing to unpack .../184-libice6_2%3a1.0.10-1build3_arm64.deb ...
241s Unpacking libice6:arm64 (2:1.0.10-1build3) ...
241s Selecting previously unselected package perl-openssl-defaults:arm64.
241s Preparing to unpack .../185-perl-openssl-defaults_7build3_arm64.deb ...
241s Unpacking perl-openssl-defaults:arm64 (7build3) ...
241s Selecting previously unselected package libnet-ssleay-perl:arm64.
241s Preparing to unpack .../186-libnet-ssleay-perl_1.94-2_arm64.deb ...
241s Unpacking libnet-ssleay-perl:arm64 (1.94-2) ...
241s Selecting previously unselected package libio-socket-ssl-perl.
241s Preparing to unpack .../187-libio-socket-ssl-perl_2.088-1_all.deb ...
241s Unpacking libio-socket-ssl-perl (2.088-1) ...
241s Selecting previously unselected package libjemalloc2:arm64.
241s Preparing to unpack .../188-libjemalloc2_5.3.0-2build1_arm64.deb ...
241s Unpacking libjemalloc2:arm64 (5.3.0-2build1) ...
241s Selecting previously unselected package libjs-bootstrap.
241s Preparing to unpack .../189-libjs-bootstrap_3.4.1+dfsg-3_all.deb ...
241s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ...
241s Selecting previously unselected package libjs-popper.js.
241s Preparing to unpack .../190-libjs-popper.js_1.16.1+ds-6_all.deb ...
241s Unpacking libjs-popper.js (1.16.1+ds-6) ...
241s Selecting previously unselected package libjs-bootstrap4.
242s Preparing to unpack .../191-libjs-bootstrap4_4.6.1+dfsg1-4_all.deb ...
242s Unpacking libjs-bootstrap4 (4.6.1+dfsg1-4) ...
242s Selecting previously unselected package libjs-d3.
242s Preparing to unpack .../192-libjs-d3_3.5.17-4_all.deb ...
242s Unpacking libjs-d3 (3.5.17-4) ...
242s Selecting previously unselected package libjs-es5-shim.
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244s Selecting previously unselected package libzzip-0-13t64:arm64.
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245s Selecting previously unselected package r-base-core.
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245s Selecting previously unselected package r-cran-littler.
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246s Selecting previously unselected package node-html5shiv.
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246s Selecting previously unselected package pandoc-data.
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247s Selecting previously unselected package python3-numpy.
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247s Selecting previously unselected package python3-pysam.
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248s Selecting previously unselected package r-bioc-biocgenerics.
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248s Selecting previously unselected package r-cran-dbi.
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248s Selecting previously unselected package r-cran-vctrs.
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249s Selecting previously unselected package r-cran-memoise.
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249s Selecting previously unselected package r-cran-pkgconfig.
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249s Selecting previously unselected package r-cran-plogr.
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249s Selecting previously unselected package r-cran-cpp11.
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249s Selecting previously unselected package r-cran-rsqlite.
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249s Selecting previously unselected package r-cran-curl.
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249s Selecting previously unselected package r-cran-jsonlite.
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249s Selecting previously unselected package r-cran-mime.
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249s Selecting previously unselected package r-cran-sys.
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249s Selecting previously unselected package r-cran-askpass.
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249s Selecting previously unselected package r-cran-openssl.
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249s Selecting previously unselected package r-cran-r6.
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249s Selecting previously unselected package r-cran-httr.
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249s Unpacking r-cran-httr (1.4.7+dfsg-1) ...
249s Selecting previously unselected package r-cran-png.
250s Preparing to unpack .../284-r-cran-png_0.1-8-1build2_arm64.deb ...
250s Unpacking r-cran-png (0.1-8-1build2) ...
250s Selecting previously unselected package zlib1g-dev:arm64.
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250s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
250s Selecting previously unselected package r-bioc-zlibbioc.
250s Preparing to unpack .../286-r-bioc-zlibbioc_1.50.0+dfsg-2_all.deb ...
250s Unpacking r-bioc-zlibbioc (1.50.0+dfsg-2) ...
250s Selecting previously unselected package r-bioc-xvector.
250s Preparing to unpack .../287-r-bioc-xvector_0.44.0-1_arm64.deb ...
250s Unpacking r-bioc-xvector (0.44.0-1) ...
250s Selecting previously unselected package r-bioc-ucsc.utils.
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250s Unpacking r-bioc-ucsc.utils (1.0.0+ds-2) ...
250s Selecting previously unselected package r-bioc-genomeinfodbdata.
250s Preparing to unpack .../289-r-bioc-genomeinfodbdata_1.2.12-1_all.deb ...
250s Unpacking r-bioc-genomeinfodbdata (1.2.12-1) ...
250s Selecting previously unselected package r-bioc-genomeinfodb.
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250s Unpacking r-bioc-genomeinfodb (1.40.1+dfsg-1) ...
250s Selecting previously unselected package r-cran-crayon.
250s Preparing to unpack .../291-r-cran-crayon_1.5.2-1_all.deb ...
250s Unpacking r-cran-crayon (1.5.2-1) ...
250s Selecting previously unselected package r-bioc-biostrings.
250s Preparing to unpack .../292-r-bioc-biostrings_2.72.1+dfsg-1_arm64.deb ...
250s Unpacking r-bioc-biostrings (2.72.1+dfsg-1) ...
250s Selecting previously unselected package r-bioc-keggrest.
250s Preparing to unpack .../293-r-bioc-keggrest_1.44.1+dfsg-1_all.deb ...
250s Unpacking r-bioc-keggrest (1.44.1+dfsg-1) ...
250s Selecting previously unselected package r-bioc-annotationdbi.
250s Preparing to unpack .../294-r-bioc-annotationdbi_1.66.0-1_all.deb ...
250s Unpacking r-bioc-annotationdbi (1.66.0-1) ...
250s Selecting previously unselected package r-cran-xml.
250s Preparing to unpack .../295-r-cran-xml_3.99-0.17-1_arm64.deb ...
250s Unpacking r-cran-xml (3.99-0.17-1) ...
250s Selecting previously unselected package r-cran-xtable.
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250s Unpacking r-cran-xtable (1:1.8-4-2) ...
251s Selecting previously unselected package r-bioc-annotate.
251s Preparing to unpack .../297-r-bioc-annotate_1.82.0+dfsg-1_all.deb ...
251s Unpacking r-bioc-annotate (1.82.0+dfsg-1) ...
251s Selecting previously unselected package r-cran-generics.
251s Preparing to unpack .../298-r-cran-generics_0.1.3-1_all.deb ...
251s Unpacking r-cran-generics (0.1.3-1) ...
251s Selecting previously unselected package r-cran-magrittr.
251s Preparing to unpack .../299-r-cran-magrittr_2.0.3-1_arm64.deb ...
251s Unpacking r-cran-magrittr (2.0.3-1) ...
251s Selecting previously unselected package r-cran-fansi.
251s Preparing to unpack .../300-r-cran-fansi_1.0.5-1_arm64.deb ...
251s Unpacking r-cran-fansi (1.0.5-1) ...
251s Selecting previously unselected package r-cran-utf8.
251s Preparing to unpack .../301-r-cran-utf8_1.2.4-1_arm64.deb ...
251s Unpacking r-cran-utf8 (1.2.4-1) ...
251s Selecting previously unselected package r-cran-pillar.
251s Preparing to unpack .../302-r-cran-pillar_1.9.0+dfsg-1_all.deb ...
251s Unpacking r-cran-pillar (1.9.0+dfsg-1) ...
251s Selecting previously unselected package r-cran-tibble.
251s Preparing to unpack .../303-r-cran-tibble_3.2.1+dfsg-2_arm64.deb ...
251s Unpacking r-cran-tibble (3.2.1+dfsg-2) ...
251s Selecting previously unselected package r-cran-withr.
251s Preparing to unpack .../304-r-cran-withr_3.0.0+dfsg-1_all.deb ...
251s Unpacking r-cran-withr (3.0.0+dfsg-1) ...
251s Selecting previously unselected package r-cran-tidyselect.
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251s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ...
251s Selecting previously unselected package r-cran-dplyr.
251s Preparing to unpack .../306-r-cran-dplyr_1.1.4-1_arm64.deb ...
251s Unpacking r-cran-dplyr (1.1.4-1) ...
251s Selecting previously unselected package r-cran-purrr.
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251s Selecting previously unselected package r-cran-stringi.
251s Preparing to unpack .../308-r-cran-stringi_1.8.3-1_arm64.deb ...
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251s Selecting previously unselected package r-cran-stringr.
251s Preparing to unpack .../309-r-cran-stringr_1.5.1-1_all.deb ...
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251s Selecting previously unselected package r-cran-tidyr.
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251s Selecting previously unselected package r-cran-dbplyr.
251s Preparing to unpack .../311-r-cran-dbplyr_2.4.0+dfsg-1_all.deb ...
251s Unpacking r-cran-dbplyr (2.4.0+dfsg-1) ...
252s Selecting previously unselected package r-cran-filelock.
252s Preparing to unpack .../312-r-cran-filelock_1.0.3-1_arm64.deb ...
252s Unpacking r-cran-filelock (1.0.3-1) ...
252s Selecting previously unselected package r-bioc-biocfilecache.
252s Preparing to unpack .../313-r-bioc-biocfilecache_2.12.0+dfsg-1_all.deb ...
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252s Selecting previously unselected package r-bioc-biocio.
252s Preparing to unpack .../314-r-bioc-biocio_1.14.0+dfsg-1_all.deb ...
252s Unpacking r-bioc-biocio (1.14.0+dfsg-1) ...
252s Selecting previously unselected package r-cran-formatr.
252s Preparing to unpack .../315-r-cran-formatr_1.14-2_all.deb ...
252s Unpacking r-cran-formatr (1.14-2) ...
252s Selecting previously unselected package r-cran-lambda.r.
252s Preparing to unpack .../316-r-cran-lambda.r_1.2.4-2build1_all.deb ...
252s Unpacking r-cran-lambda.r (1.2.4-2build1) ...
252s Selecting previously unselected package r-cran-futile.options.
252s Preparing to unpack .../317-r-cran-futile.options_1.0.1-3build1_all.deb ...
252s Unpacking r-cran-futile.options (1.0.1-3build1) ...
252s Selecting previously unselected package r-cran-futile.logger.
252s Preparing to unpack .../318-r-cran-futile.logger_1.4.3-4build1_all.deb ...
252s Unpacking r-cran-futile.logger (1.4.3-4build1) ...
252s Selecting previously unselected package r-cran-snow.
252s Preparing to unpack .../319-r-cran-snow_1%3a0.4.4-2_all.deb ...
252s Unpacking r-cran-snow (1:0.4.4-2) ...
252s Selecting previously unselected package r-cran-codetools.
252s Preparing to unpack .../320-r-cran-codetools_0.2-20-1_all.deb ...
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252s Selecting previously unselected package r-cran-bh.
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252s Unpacking r-cran-bh (1.84.0-1) ...
252s Selecting previously unselected package r-bioc-biocparallel.
252s Preparing to unpack .../322-r-bioc-biocparallel_1.38.0-2_arm64.deb ...
252s Unpacking r-bioc-biocparallel (1.38.0-2) ...
252s Selecting previously unselected package r-cran-base64enc.
252s Preparing to unpack .../323-r-cran-base64enc_0.1-3-3_arm64.deb ...
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252s Selecting previously unselected package r-cran-digest.
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252s Selecting previously unselected package r-cran-htmltools.
252s Preparing to unpack .../325-r-cran-htmltools_0.5.8.1-1_arm64.deb ...
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252s Selecting previously unselected package r-cran-evaluate.
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252s Selecting previously unselected package r-cran-xfun.
252s Preparing to unpack .../327-r-cran-xfun_0.45+dfsg-1_arm64.deb ...
252s Unpacking r-cran-xfun (0.45+dfsg-1) ...
252s Selecting previously unselected package r-cran-highr.
252s Preparing to unpack .../328-r-cran-highr_0.11+dfsg-1_all.deb ...
252s Unpacking r-cran-highr (0.11+dfsg-1) ...
253s Selecting previously unselected package r-cran-yaml.
253s Preparing to unpack .../329-r-cran-yaml_2.3.8-2_arm64.deb ...
253s Unpacking r-cran-yaml (2.3.8-2) ...
253s Selecting previously unselected package libjs-mathjax.
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253s Selecting previously unselected package r-cran-knitr.
253s Preparing to unpack .../331-r-cran-knitr_1.47+dfsg-1_all.deb ...
253s Unpacking r-cran-knitr (1.47+dfsg-1) ...
253s Selecting previously unselected package r-cran-jquerylib.
253s Preparing to unpack .../332-r-cran-jquerylib_0.1.4+dfsg-4_all.deb ...
253s Unpacking r-cran-jquerylib (0.1.4+dfsg-4) ...
253s Selecting previously unselected package r-cran-fs.
253s Preparing to unpack .../333-r-cran-fs_1.6.4+dfsg-1_arm64.deb ...
253s Unpacking r-cran-fs (1.6.4+dfsg-1) ...
253s Selecting previously unselected package r-cran-rappdirs.
254s Preparing to unpack .../334-r-cran-rappdirs_0.3.3-1_arm64.deb ...
254s Unpacking r-cran-rappdirs (0.3.3-1) ...
254s Selecting previously unselected package r-cran-sass.
254s Preparing to unpack .../335-r-cran-sass_0.4.9+dfsg-1_arm64.deb ...
254s Unpacking r-cran-sass (0.4.9+dfsg-1) ...
254s Selecting previously unselected package r-cran-bslib.
254s Preparing to unpack .../336-r-cran-bslib_0.7.0+dfsg-1_all.deb ...
254s Unpacking r-cran-bslib (0.7.0+dfsg-1) ...
254s Selecting previously unselected package r-cran-fontawesome.
254s Preparing to unpack .../337-r-cran-fontawesome_0.5.2-1_all.deb ...
254s Unpacking r-cran-fontawesome (0.5.2-1) ...
254s Selecting previously unselected package r-cran-tinytex.
254s Preparing to unpack .../338-r-cran-tinytex_0.51-1_all.deb ...
254s Unpacking r-cran-tinytex (0.51-1) ...
254s Selecting previously unselected package libjs-modernizr.
254s Preparing to unpack .../339-libjs-modernizr_3.13.0-0.1_all.deb ...
254s Unpacking libjs-modernizr (3.13.0-0.1) ...
254s Selecting previously unselected package r-cran-pkgkitten.
254s Preparing to unpack .../340-r-cran-pkgkitten_0.2.3-1_all.deb ...
254s Unpacking r-cran-pkgkitten (0.2.3-1) ...
254s Selecting previously unselected package r-cran-rcpp.
254s Preparing to unpack .../341-r-cran-rcpp_1.0.13-1_arm64.deb ...
254s Unpacking r-cran-rcpp (1.0.13-1) ...
254s Selecting previously unselected package r-cran-later.
254s Preparing to unpack .../342-r-cran-later_1.3.2+dfsg-1_arm64.deb ...
254s Unpacking r-cran-later (1.3.2+dfsg-1) ...
254s Selecting previously unselected package r-cran-promises.
254s Preparing to unpack .../343-r-cran-promises_1.3.0+dfsg-1_arm64.deb ...
254s Unpacking r-cran-promises (1.3.0+dfsg-1) ...
254s Selecting previously unselected package r-cran-httpuv.
254s Preparing to unpack .../344-r-cran-httpuv_1.6.15+dfsg-1_arm64.deb ...
254s Unpacking r-cran-httpuv (1.6.15+dfsg-1) ...
255s Selecting previously unselected package r-cran-sourcetools.
255s Preparing to unpack .../345-r-cran-sourcetools_0.1.7-1-1_arm64.deb ...
255s Unpacking r-cran-sourcetools (0.1.7-1-1) ...
255s Selecting previously unselected package r-cran-commonmark.
255s Preparing to unpack .../346-r-cran-commonmark_1.9.1-1_arm64.deb ...
255s Unpacking r-cran-commonmark (1.9.1-1) ...
255s Selecting previously unselected package libjs-twitter-bootstrap-datepicker.
255s Preparing to unpack .../347-libjs-twitter-bootstrap-datepicker_1.3.1+dfsg1-4.1_all.deb ...
255s Unpacking libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ...
255s Selecting previously unselected package r-cran-shiny.
255s Preparing to unpack .../348-r-cran-shiny_1.8.1.1+dfsg-1_all.deb ...
255s Unpacking r-cran-shiny (1.8.1.1+dfsg-1) ...
255s Selecting previously unselected package r-cran-rmarkdown.
255s Preparing to unpack .../349-r-cran-rmarkdown_2.27+dfsg-1_all.deb ...
255s Unpacking r-cran-rmarkdown (2.27+dfsg-1) ...
255s Selecting previously unselected package r-cran-bookdown.
255s Preparing to unpack .../350-r-cran-bookdown_0.40+dfsg-1_all.deb ...
255s Unpacking r-cran-bookdown (0.40+dfsg-1) ...
255s Selecting previously unselected package r-cran-biocmanager.
255s Preparing to unpack .../351-r-cran-biocmanager_1.30.22+dfsg-2_all.deb ...
255s Unpacking r-cran-biocmanager (1.30.22+dfsg-2) ...
255s Selecting previously unselected package tex-common.
255s Preparing to unpack .../352-tex-common_6.18_all.deb ...
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255s Selecting previously unselected package t1utils.
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255s Unpacking t1utils (1.41-4build3) ...
255s Selecting previously unselected package texlive-binaries.
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256s Unpacking texlive-base (2024.20240706-1) ...
257s Selecting previously unselected package texlive-latex-base.
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257s Unpacking texlive-latex-base (2024.20240706-1) ...
257s Selecting previously unselected package texlive-bibtex-extra.
257s Preparing to unpack .../357-texlive-bibtex-extra_2024.20240706-2_all.deb ...
257s Unpacking texlive-bibtex-extra (2024.20240706-2) ...
260s Selecting previously unselected package r-bioc-biocversion.
260s Preparing to unpack .../358-r-bioc-biocversion_3.19.1-1_all.deb ...
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260s Selecting previously unselected package r-bioc-biocstyle.
260s Preparing to unpack .../359-r-bioc-biocstyle_2.32.1+dfsg-1_all.deb ...
260s Unpacking r-bioc-biocstyle (2.32.1+dfsg-1) ...
260s Selecting previously unselected package r-cran-hms.
260s Preparing to unpack .../360-r-cran-hms_1.1.3-1_all.deb ...
260s Unpacking r-cran-hms (1.1.3-1) ...
260s Selecting previously unselected package r-cran-prettyunits.
260s Preparing to unpack .../361-r-cran-prettyunits_1.2.0-1_all.deb ...
260s Unpacking r-cran-prettyunits (1.2.0-1) ...
260s Selecting previously unselected package r-cran-progress.
260s Preparing to unpack .../362-r-cran-progress_1.2.3-1_all.deb ...
260s Unpacking r-cran-progress (1.2.3-1) ...
260s Selecting previously unselected package r-cran-httr2.
260s Preparing to unpack .../363-r-cran-httr2_1.0.2-1_all.deb ...
260s Unpacking r-cran-httr2 (1.0.2-1) ...
260s Selecting previously unselected package r-cran-xml2.
260s Preparing to unpack .../364-r-cran-xml2_1.3.6-1_arm64.deb ...
260s Unpacking r-cran-xml2 (1.3.6-1) ...
260s Selecting previously unselected package r-bioc-biomart.
260s Preparing to unpack .../365-r-bioc-biomart_2.60.1+dfsg-1_all.deb ...
260s Unpacking r-bioc-biomart (2.60.1+dfsg-1) ...
260s Selecting previously unselected package r-cran-lattice.
260s Preparing to unpack .../366-r-cran-lattice_0.22-6-1_arm64.deb ...
260s Unpacking r-cran-lattice (0.22-6-1) ...
260s Selecting previously unselected package r-cran-matrix.
260s Preparing to unpack .../367-r-cran-matrix_1.7-0-3_arm64.deb ...
260s Unpacking r-cran-matrix (1.7-0-3) ...
260s Selecting previously unselected package r-cran-matrixstats.
260s Preparing to unpack .../368-r-cran-matrixstats_1.3.0-1_arm64.deb ...
260s Unpacking r-cran-matrixstats (1.3.0-1) ...
260s Selecting previously unselected package r-bioc-matrixgenerics.
260s Preparing to unpack .../369-r-bioc-matrixgenerics_1.16.0-2_all.deb ...
260s Unpacking r-bioc-matrixgenerics (1.16.0-2) ...
260s Selecting previously unselected package r-cran-abind.
260s Preparing to unpack .../370-r-cran-abind_1.4-5-2_all.deb ...
260s Unpacking r-cran-abind (1.4-5-2) ...
260s Selecting previously unselected package r-bioc-s4arrays.
260s Preparing to unpack .../371-r-bioc-s4arrays_1.4.1+dfsg-1_arm64.deb ...
260s Unpacking r-bioc-s4arrays (1.4.1+dfsg-1) ...
260s Selecting previously unselected package r-bioc-sparsearray.
261s Preparing to unpack .../372-r-bioc-sparsearray_1.4.8+dfsg-1_arm64.deb ...
261s Unpacking r-bioc-sparsearray (1.4.8+dfsg-1) ...
261s Selecting previously unselected package r-bioc-delayedarray.
261s Preparing to unpack .../373-r-bioc-delayedarray_0.30.1+dfsg-1_arm64.deb ...
261s Unpacking r-bioc-delayedarray (0.30.1+dfsg-1) ...
261s Selecting previously unselected package r-bioc-genomicranges.
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261s Unpacking r-bioc-genomicranges (1.56.1+dfsg-1) ...
261s Selecting previously unselected package r-bioc-summarizedexperiment.
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261s Unpacking r-bioc-summarizedexperiment (1.34.0+dfsg-1) ...
261s Selecting previously unselected package r-cran-locfit.
261s Preparing to unpack .../376-r-cran-locfit_1.5-9.9-1_arm64.deb ...
261s Unpacking r-cran-locfit (1.5-9.9-1) ...
261s Selecting previously unselected package r-cran-gtable.
261s Preparing to unpack .../377-r-cran-gtable_0.3.5+dfsg-1_all.deb ...
261s Unpacking r-cran-gtable (0.3.5+dfsg-1) ...
261s Selecting previously unselected package r-cran-isoband.
261s Preparing to unpack .../378-r-cran-isoband_0.2.7-1_arm64.deb ...
261s Unpacking r-cran-isoband (0.2.7-1) ...
261s Selecting previously unselected package r-cran-mass.
261s Preparing to unpack .../379-r-cran-mass_7.3-61-1_arm64.deb ...
261s Unpacking r-cran-mass (7.3-61-1) ...
261s Selecting previously unselected package r-cran-nlme.
261s Preparing to unpack .../380-r-cran-nlme_3.1.166-1_arm64.deb ...
261s Unpacking r-cran-nlme (3.1.166-1) ...
261s Selecting previously unselected package r-cran-mgcv.
261s Preparing to unpack .../381-r-cran-mgcv_1.9-1-1_arm64.deb ...
261s Unpacking r-cran-mgcv (1.9-1-1) ...
261s Selecting previously unselected package r-cran-farver.
261s Preparing to unpack .../382-r-cran-farver_2.1.2-1_arm64.deb ...
261s Unpacking r-cran-farver (2.1.2-1) ...
261s Selecting previously unselected package r-cran-labeling.
261s Preparing to unpack .../383-r-cran-labeling_0.4.3-1_all.deb ...
261s Unpacking r-cran-labeling (0.4.3-1) ...
261s Selecting previously unselected package r-cran-colorspace.
261s Preparing to unpack .../384-r-cran-colorspace_2.1-0+dfsg-1_arm64.deb ...
261s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ...
261s Selecting previously unselected package r-cran-munsell.
262s Preparing to unpack .../385-r-cran-munsell_0.5.1-1_all.deb ...
262s Unpacking r-cran-munsell (0.5.1-1) ...
262s Selecting previously unselected package r-cran-rcolorbrewer.
262s Preparing to unpack .../386-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ...
262s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ...
262s Selecting previously unselected package r-cran-viridislite.
262s Preparing to unpack .../387-r-cran-viridislite_0.4.2-2_all.deb ...
262s Unpacking r-cran-viridislite (0.4.2-2) ...
262s Selecting previously unselected package r-cran-scales.
262s Preparing to unpack .../388-r-cran-scales_1.3.0-1_all.deb ...
262s Unpacking r-cran-scales (1.3.0-1) ...
262s Selecting previously unselected package r-cran-ggplot2.
262s Preparing to unpack .../389-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ...
262s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ...
262s Selecting previously unselected package r-cran-rcpparmadillo.
262s Preparing to unpack .../390-r-cran-rcpparmadillo_14.0.0-1-1_arm64.deb ...
262s Unpacking r-cran-rcpparmadillo (14.0.0-1-1) ...
262s Selecting previously unselected package r-bioc-deseq2.
262s Preparing to unpack .../391-r-bioc-deseq2_1.44.0+dfsg-1_arm64.deb ...
262s Unpacking r-bioc-deseq2 (1.44.0+dfsg-1) ...
262s Selecting previously unselected package r-cran-hwriter.
262s Preparing to unpack .../392-r-cran-hwriter_1.3.2.1-1_all.deb ...
262s Unpacking r-cran-hwriter (1.3.2.1-1) ...
262s Selecting previously unselected package r-cran-bitops.
262s Preparing to unpack .../393-r-cran-bitops_1.0-7-1_arm64.deb ...
262s Unpacking r-cran-bitops (1.0-7-1) ...
262s Selecting previously unselected package r-bioc-rhtslib.
262s Preparing to unpack .../394-r-bioc-rhtslib_3.0.0+dfsg-1_arm64.deb ...
262s Unpacking r-bioc-rhtslib (3.0.0+dfsg-1) ...
262s Selecting previously unselected package r-bioc-rsamtools.
262s Preparing to unpack .../395-r-bioc-rsamtools_2.20.0+dfsg-1_arm64.deb ...
262s Unpacking r-bioc-rsamtools (2.20.0+dfsg-1) ...
262s Selecting previously unselected package r-cran-statmod.
263s Preparing to unpack .../396-r-cran-statmod_1.5.0-1_arm64.deb ...
263s Unpacking r-cran-statmod (1.5.0-1) ...
263s Selecting previously unselected package r-bioc-geneplotter.
263s Preparing to unpack .../397-r-bioc-geneplotter_1.82.0+dfsg-1_all.deb ...
263s Unpacking r-bioc-geneplotter (1.82.0+dfsg-1) ...
263s Selecting previously unselected package r-cran-survival.
263s Preparing to unpack .../398-r-cran-survival_3.7-0-1_arm64.deb ...
263s Unpacking r-cran-survival (3.7-0-1) ...
263s Selecting previously unselected package r-bioc-genefilter.
263s Preparing to unpack .../399-r-bioc-genefilter_1.86.0-1_arm64.deb ...
263s Unpacking r-bioc-genefilter (1.86.0-1) ...
263s Selecting previously unselected package r-bioc-dexseq.
263s Preparing to unpack .../400-r-bioc-dexseq_1.50.0+dfsg-1_all.deb ...
263s Unpacking r-bioc-dexseq (1.50.0+dfsg-1) ...
263s Selecting previously unselected package r-bioc-limma.
263s Preparing to unpack .../401-r-bioc-limma_3.60.4+dfsg-1_arm64.deb ...
263s Unpacking r-bioc-limma (3.60.4+dfsg-1) ...
263s Selecting previously unselected package r-bioc-edger.
263s Preparing to unpack .../402-r-bioc-edger_4.2.1+dfsg-1_arm64.deb ...
263s Unpacking r-bioc-edger (4.2.1+dfsg-1) ...
263s Selecting previously unselected package r-bioc-genomicalignments.
263s Preparing to unpack .../403-r-bioc-genomicalignments_1.40.0-1_arm64.deb ...
263s Unpacking r-bioc-genomicalignments (1.40.0-1) ...
263s Selecting previously unselected package r-cran-rcurl.
263s Preparing to unpack .../404-r-cran-rcurl_1.98-1.14+dfsg-1build2_arm64.deb ...
263s Unpacking r-cran-rcurl (1.98-1.14+dfsg-1build2) ...
263s Selecting previously unselected package r-cran-rjson.
263s Preparing to unpack .../405-r-cran-rjson_0.2.21-1_arm64.deb ...
263s Unpacking r-cran-rjson (0.2.21-1) ...
263s Selecting previously unselected package r-cran-restfulr.
263s Preparing to unpack .../406-r-cran-restfulr_0.0.15-1_arm64.deb ...
263s Unpacking r-cran-restfulr (0.0.15-1) ...
263s Selecting previously unselected package r-bioc-rtracklayer.
263s Preparing to unpack .../407-r-bioc-rtracklayer_1.64.0-1_arm64.deb ...
263s Unpacking r-bioc-rtracklayer (1.64.0-1) ...
263s Selecting previously unselected package r-bioc-genomicfeatures.
263s Preparing to unpack .../408-r-bioc-genomicfeatures_1.56.0+dfsg-1_all.deb ...
263s Unpacking r-bioc-genomicfeatures (1.56.0+dfsg-1) ...
263s Selecting previously unselected package r-bioc-txdbmaker.
264s Preparing to unpack .../409-r-bioc-txdbmaker_1.0.1+ds-1_all.deb ...
264s Unpacking r-bioc-txdbmaker (1.0.1+ds-1) ...
264s Selecting previously unselected package r-bioc-genelendatabase.
264s Preparing to unpack .../410-r-bioc-genelendatabase_1.40.1-1_all.deb ...
264s Unpacking r-bioc-genelendatabase (1.40.1-1) ...
264s Selecting previously unselected package r-bioc-go.db.
264s Preparing to unpack .../411-r-bioc-go.db_3.19.1-1_all.deb ...
264s Unpacking r-bioc-go.db (3.19.1-1) ...
265s Selecting previously unselected package r-cran-biasedurn.
265s Preparing to unpack .../412-r-cran-biasedurn_2.0.11-1_arm64.deb ...
265s Unpacking r-cran-biasedurn (2.0.11-1) ...
265s Selecting previously unselected package r-bioc-goseq.
265s Preparing to unpack .../413-r-bioc-goseq_1.56.0-1_all.deb ...
265s Unpacking r-bioc-goseq (1.56.0-1) ...
265s Selecting previously unselected package r-cran-plyr.
265s Preparing to unpack .../414-r-cran-plyr_1.8.9-1_arm64.deb ...
265s Unpacking r-cran-plyr (1.8.9-1) ...
265s Selecting previously unselected package r-cran-reshape2.
265s Preparing to unpack .../415-r-cran-reshape2_1.4.4-2build1_arm64.deb ...
265s Unpacking r-cran-reshape2 (1.4.4-2build1) ...
265s Selecting previously unselected package r-bioc-qvalue.
265s Preparing to unpack .../416-r-bioc-qvalue_2.36.0-1_all.deb ...
265s Unpacking r-bioc-qvalue (2.36.0-1) ...
265s Selecting previously unselected package r-cran-findpython.
265s Preparing to unpack .../417-r-cran-findpython_1.0.8-1_all.deb ...
265s Unpacking r-cran-findpython (1.0.8-1) ...
265s Selecting previously unselected package r-cran-argparse.
265s Preparing to unpack .../418-r-cran-argparse_2.2.3+dfsg-1_all.deb ...
265s Unpacking r-cran-argparse (2.2.3+dfsg-1) ...
265s Selecting previously unselected package r-cran-backports.
265s Preparing to unpack .../419-r-cran-backports_1.5.0-2_arm64.deb ...
265s Unpacking r-cran-backports (1.5.0-2) ...
265s Selecting previously unselected package r-cran-broom.
265s Preparing to unpack .../420-r-cran-broom_1.0.6+dfsg-1_all.deb ...
265s Unpacking r-cran-broom (1.0.6+dfsg-1) ...
265s Selecting previously unselected package r-cran-ps.
265s Preparing to unpack .../421-r-cran-ps_1.7.6-1_arm64.deb ...
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265s Selecting previously unselected package r-cran-processx.
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265s Selecting previously unselected package r-cran-callr.
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265s Selecting previously unselected package r-cran-rematch.
265s Preparing to unpack .../424-r-cran-rematch_2.0.0-1_all.deb ...
265s Unpacking r-cran-rematch (2.0.0-1) ...
265s Selecting previously unselected package r-cran-cellranger.
265s Preparing to unpack .../425-r-cran-cellranger_1.1.0-3_all.deb ...
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265s Selecting previously unselected package r-cran-clipr.
265s Preparing to unpack .../426-r-cran-clipr_0.8.0-1_all.deb ...
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265s Selecting previously unselected package r-cran-cluster.
266s Preparing to unpack .../427-r-cran-cluster_2.1.6-1build1_arm64.deb ...
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266s Selecting previously unselected package r-cran-conflicted.
266s Preparing to unpack .../428-r-cran-conflicted_1.2.0-1.1_all.deb ...
266s Unpacking r-cran-conflicted (1.2.0-1.1) ...
266s Selecting previously unselected package r-cran-data.table.
266s Preparing to unpack .../429-r-cran-data.table_1.15.4+dfsg-2.2_arm64.deb ...
266s Unpacking r-cran-data.table (1.15.4+dfsg-2.2) ...
266s Selecting previously unselected package r-cran-dtplyr.
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266s Unpacking r-cran-dtplyr (1.3.1-1) ...
266s Selecting previously unselected package r-cran-ellipsis.
266s Preparing to unpack .../431-r-cran-ellipsis_0.3.2-2_arm64.deb ...
266s Unpacking r-cran-ellipsis (0.3.2-2) ...
266s Selecting previously unselected package r-cran-fastcluster.
266s Preparing to unpack .../432-r-cran-fastcluster_1.2.6-1build1_arm64.deb ...
266s Unpacking r-cran-fastcluster (1.2.6-1build1) ...
266s Selecting previously unselected package r-cran-forcats.
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266s Unpacking r-cran-forcats (1.0.0-1) ...
266s Selecting previously unselected package r-cran-gargle.
266s Preparing to unpack .../434-r-cran-gargle_1.5.2-1_all.deb ...
266s Unpacking r-cran-gargle (1.5.2-1) ...
266s Selecting previously unselected package r-cran-ggdendro.
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266s Unpacking r-cran-ggdendro (0.2.0+dfsg-1) ...
266s Selecting previously unselected package r-cran-uuid.
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266s Unpacking r-cran-uuid (1.2-1-1) ...
266s Selecting previously unselected package r-cran-googledrive.
266s Preparing to unpack .../437-r-cran-googledrive_2.1.1-1_all.deb ...
266s Unpacking r-cran-googledrive (2.1.1-1) ...
266s Selecting previously unselected package r-cran-ids.
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266s Unpacking r-cran-ids (1.0.1-2) ...
266s Selecting previously unselected package r-cran-rematch2.
266s Preparing to unpack .../439-r-cran-rematch2_2.1.2-2build1_all.deb ...
266s Unpacking r-cran-rematch2 (2.1.2-2build1) ...
266s Selecting previously unselected package r-cran-googlesheets4.
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266s Unpacking r-cran-googlesheets4 (1.1.1-1) ...
266s Selecting previously unselected package r-cran-gridextra.
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266s Unpacking r-cran-gridextra (2.3-3build1) ...
266s Selecting previously unselected package r-cran-goplot.
266s Preparing to unpack .../442-r-cran-goplot_1.0.2-2_all.deb ...
266s Unpacking r-cran-goplot (1.0.2-2) ...
267s Selecting previously unselected package r-cran-tzdb.
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267s Selecting previously unselected package r-cran-vroom.
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267s Selecting previously unselected package r-cran-readr.
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267s Selecting previously unselected package r-cran-haven.
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267s Selecting previously unselected package r-cran-kernsmooth.
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267s Selecting previously unselected package r-cran-timechange.
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267s Selecting previously unselected package r-cran-lubridate.
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267s Selecting previously unselected package r-cran-modelr.
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267s Selecting previously unselected package r-cran-systemfonts.
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267s Selecting previously unselected package r-cran-textshaping.
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267s Selecting previously unselected package r-cran-ragg.
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267s Selecting previously unselected package r-cran-readxl.
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267s Selecting previously unselected package r-cran-rstudioapi.
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267s Selecting previously unselected package r-cran-reprex.
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267s Selecting previously unselected package r-cran-rvest.
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268s Selecting previously unselected package r-cran-tidyverse.
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271s Setting up libhtscodecs2:arm64 (1.6.0-1build1) ...
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272s Setting up berkeley-express (1.5.3+dfsg-3build5) ...
272s Setting up libvulkan1:arm64 (1.3.290.0-1) ...
272s Setting up libwebp7:arm64 (1.4.0-0.1) ...
272s Setting up libtimedate-perl (2.3300-2) ...
272s Setting up libubsan1:arm64 (14.2.0-7ubuntu1) ...
272s Setting up libxcb-dri2-0:arm64 (1.17.0-2) ...
272s Setting up libgif7:arm64 (5.2.2-1ubuntu1) ...
272s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
272s Setting up libjs-highlight.js (9.18.5+dfsg1-2) ...
272s Setting up hisat2 (2.2.1-5) ...
272s Setting up libfreemarker-java (2.3.32-2) ...
272s Setting up libxshmfence1:arm64 (1.3-1build5) ...
272s Setting up libhwasan0:arm64 (14.2.0-7ubuntu1) ...
272s Setting up subread (2.0.6+dfsg-3) ...
272s Setting up at-spi2-common (2.54.0-1) ...
272s Setting up libxcb-randr0:arm64 (1.17.0-2) ...
272s Setting up libasan8:arm64 (14.2.0-7ubuntu1) ...
272s Setting up libhts3t64:arm64 (1.20+ds-1) ...
272s Setting up fonts-lmodern (2.005-1) ...
272s Setting up liblua5.4-0:arm64 (5.4.6-3build2) ...
272s Setting up libharfbuzz0b:arm64 (9.0.0-1) ...
272s Setting up ncbi-vdb-data (3.0.2+dfsg-2build2) ...
272s Setting up libthai-data (0.1.29-2build1) ...
272s Setting up node-bootstrap-sass (3.4.3-2) ...
272s Setting up libcommons-math3-java (3.6.1-3) ...
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272s Setting up libxss1:arm64 (1:1.2.3-1build3) ...
272s Setting up libjs-bootstrap4 (4.6.1+dfsg1-4) ...
272s Setting up libhttpcore-java (4.4.16-1) ...
272s Setting up pandoc-data (3.1.11.1-3) ...
272s Setting up libtsan2:arm64 (14.2.0-7ubuntu1) ...
272s Setting up libjoptsimple-java (5.0.4-4) ...
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272s Setting up ca-certificates-java (20240118) ...
272s No JRE found. Skipping Java certificates setup.
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272s Setting up libsnappy-jni (1.1.10.5-2) ...
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272s Setting up xdg-utils (1.2.1-0ubuntu1) ...
272s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
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272s Setting up python3-pysam (0.22.1+ds-2) ...
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272s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
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274s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
274s Setting up libwayland-cursor0:arm64 (1.23.0-1) ...
274s Setting up libhtml-parser-perl:arm64 (3.83-1build1) ...
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274s Setting up libsnappy-java (1.1.10.5-2) ...
274s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ...
274s Setting up libgcc-14-dev:arm64 (14.2.0-7ubuntu1) ...
274s Setting up libcommons-codec-java (1.16.0-1) ...
274s Setting up libstdc++-14-dev:arm64 (14.2.0-7ubuntu1) ...
274s Setting up libsm6:arm64 (2:1.2.3-1build3) ...
274s Setting up python3-htseq (2.0.5-2) ...
274s /usr/lib/python3/dist-packages/HTSeq/__init__.py:583: SyntaxWarning: invalid escape sequence '\='
274s   _re_vcf_meta_comment = re.compile("^##([a-zA-Z]+)\=(.*)$")
274s /usr/lib/python3/dist-packages/HTSeq/features.py:14: SyntaxWarning: invalid escape sequence '\s'
274s   _re_attr_main = re.compile("\s*([^\s\=]+)[\s=]+(.*)")
274s /usr/lib/python3/dist-packages/HTSeq/features.py:15: SyntaxWarning: invalid escape sequence '\s'
274s   _re_attr_empty = re.compile("^\s*$")
274s /usr/lib/python3/dist-packages/HTSeq/features.py:16: SyntaxWarning: invalid escape sequence '\s'
274s   _re_gff_meta_comment = re.compile("##\s*(\S+)\s+(\S*)")
274s Setting up libavahi-client3:arm64 (0.8-13ubuntu6) ...
274s Setting up libio-socket-ssl-perl (2.088-1) ...
274s Setting up libhttp-message-perl (6.46-1ubuntu1) ...
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274s Setting up gtk-update-icon-cache (4.16.2+ds-2) ...
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277s Setting up libhttp-cookies-perl (6.11-1) ...
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277s Setting up libcairo2:arm64 (1.18.2-2) ...
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277s Setting up libpangocairo-1.0-0:arm64 (1.54.0+ds-2) ...
277s Setting up libncbi-ngs3:arm64 (3.0.3+dfsg-9ubuntu1) ...
277s Setting up libngs-jni:arm64 (3.0.3+dfsg-9ubuntu1) ...
277s Setting up libxmu6:arm64 (2:1.1.3-3build2) ...
277s Setting up liblog4j2-java (2.19.0-2) ...
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277s Setting up r-base-core (4.4.1-1) ...
277s 
277s Creating config file /etc/R/Renviron with new version
277s Setting up r-cran-crayon (1.5.2-1) ...
277s Setting up r-cran-labeling (0.4.3-1) ...
277s Setting up r-cran-biasedurn (2.0.11-1) ...
277s Setting up r-cran-sourcetools (0.1.7-1-1) ...
277s Setting up r-cran-futile.options (1.0.1-3build1) ...
277s Setting up r-cran-lattice (0.22-6-1) ...
277s Setting up r-cran-ps (1.7.6-1) ...
277s Setting up r-cran-nlme (3.1.166-1) ...
277s Setting up r-cran-farver (2.1.2-1) ...
277s Setting up r-cran-formatr (1.14-2) ...
277s Setting up r-cran-xml (3.99-0.17-1) ...
277s Setting up trinityrnaseq-examples (2.15.1+dfsg-5build1) ...
277s Setting up r-cran-viridislite (0.4.2-2) ...
277s Setting up r-cran-locfit (1.5-9.9-1) ...
277s Setting up texlive-binaries (2024.20240313.70630+ds-4) ...
277s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
277s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
277s Setting up r-cran-cluster (2.1.6-1build1) ...
277s Setting up rsem (1.3.3+dfsg-3build1) ...
277s Setting up r-cran-statmod (1.5.0-1) ...
277s Setting up r-cran-clipr (0.8.0-1) ...
277s Setting up r-cran-commonmark (1.9.1-1) ...
277s Setting up libngs-java:arm64 (3.0.3+dfsg-9ubuntu1) ...
277s Setting up r-cran-r6 (2.5.1-1) ...
277s Setting up r-cran-pkgkitten (0.2.3-1) ...
277s Setting up r-cran-fastcluster (1.2.6-1build1) ...
277s Setting up texlive-base (2024.20240706-1) ...
277s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps
278s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg
278s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper
278s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex
279s Setting up r-cran-magrittr (2.0.3-1) ...
279s Setting up r-cran-rappdirs (0.3.3-1) ...
279s Setting up r-cran-filelock (1.0.3-1) ...
279s Setting up libhtsjdk-java (4.1.0+dfsg-2) ...
279s Setting up libbarclay-java (5.0.0+dfsg-1) ...
279s Setting up r-bioc-genomeinfodbdata (1.2.12-1) ...
279s Setting up r-cran-littler (0.3.20-1) ...
279s Setting up r-cran-bh (1.84.0-1) ...
279s Setting up r-cran-fs (1.6.4+dfsg-1) ...
279s Setting up r-cran-rcpp (1.0.13-1) ...
279s Setting up r-cran-curl (5.2.1+dfsg-1) ...
279s Setting up r-cran-codetools (0.2-20-1) ...
279s Setting up r-cran-rematch (2.0.0-1) ...
279s Setting up r-bioc-biocgenerics (0.50.0-2) ...
279s Setting up r-cran-rlang (1.1.4-1) ...
279s Setting up r-cran-matrixstats (1.3.0-1) ...
279s Setting up r-cran-findpython (1.0.8-1) ...
279s Setting up littler (0.3.20-1) ...
279s Setting up r-bioc-matrixgenerics (1.16.0-2) ...
279s Setting up r-cran-uuid (1.2-1-1) ...
279s Setting up r-cran-xfun (0.45+dfsg-1) ...
279s Setting up r-cran-sys (3.4.2-1) ...
279s Setting up r-cran-plogr (0.2.0-3build1) ...
279s Setting up r-cran-withr (3.0.0+dfsg-1) ...
279s Setting up r-cran-backports (1.5.0-2) ...
279s Setting up libgkl-java (0.8.11+dfsg-2build1) ...
279s Setting up r-cran-processx (3.8.4-1) ...
279s Setting up r-cran-mime (0.12-2) ...
279s Setting up r-cran-generics (0.1.3-1) ...
279s Setting up r-cran-base64enc (0.1-3-3) ...
279s Setting up r-cran-abind (1.4-5-2) ...
279s Setting up r-cran-digest (0.6.36-1) ...
279s Setting up r-cran-yaml (2.3.8-2) ...
279s Setting up r-cran-lambda.r (1.2.4-2build1) ...
279s Setting up r-cran-evaluate (0.24.0-1) ...
279s Setting up r-cran-dbi (1.2.3-1) ...
279s Setting up r-cran-highr (0.11+dfsg-1) ...
279s Setting up r-cran-prettyunits (1.2.0-1) ...
279s Setting up r-cran-fansi (1.0.5-1) ...
279s Setting up r-cran-mass (7.3-61-1) ...
279s Setting up r-cran-snow (1:0.4.4-2) ...
279s Setting up r-cran-data.table (1.15.4+dfsg-2.2) ...
279s Setting up r-cran-glue (1.7.0-1) ...
279s Setting up r-cran-bit (4.0.5-1) ...
279s Setting up r-cran-xtable (1:1.8-4-2) ...
279s Setting up r-cran-cli (3.6.2-1) ...
279s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
279s Setting up r-cran-bitops (1.0-7-1) ...
279s Setting up r-bioc-biocversion (3.19.1-1) ...
279s Setting up r-cran-bit64 (4.0.5-1) ...
279s Setting up r-cran-biocmanager (1.30.22+dfsg-2) ...
279s Setting up r-bioc-zlibbioc (1.50.0+dfsg-2) ...
279s Setting up r-cran-askpass (1.2.0-1) ...
279s Setting up r-cran-fastmap (1.1.1-1) ...
279s Setting up r-cran-png (0.1-8-1build2) ...
279s Setting up r-bioc-biobase (2.64.0-4) ...
279s Setting up r-cran-jsonlite (1.8.8+dfsg-1) ...
279s Setting up r-cran-rstudioapi (0.16.0-1) ...
279s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
279s Setting up libpicard-java (3.1.1+dfsg-1) ...
279s Setting up r-cran-utf8 (1.2.4-1) ...
279s Setting up r-cran-colorspace (2.1-0+dfsg-1) ...
279s Setting up r-cran-stringi (1.8.3-1) ...
279s Setting up texlive-latex-base (2024.20240706-1) ...
279s Setting up r-cran-hwriter (1.3.2.1-1) ...
279s Setting up r-cran-cpp11 (0.4.7-1) ...
279s Setting up r-cran-plyr (1.8.9-1) ...
279s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ...
279s Setting up r-bioc-s4vectors (0.42.1+dfsg-2) ...
279s Setting up r-cran-isoband (0.2.7-1) ...
279s Setting up r-cran-futile.logger (1.4.3-4build1) ...
279s Setting up r-bioc-limma (3.60.4+dfsg-1) ...
279s Setting up r-cran-gtable (0.3.5+dfsg-1) ...
279s Setting up r-cran-later (1.3.2+dfsg-1) ...
279s Setting up r-cran-matrix (1.7-0-3) ...
279s Setting up r-cran-htmltools (0.5.8.1-1) ...
279s Setting up r-cran-tinytex (0.51-1) ...
279s Setting up r-cran-kernsmooth (2.23-24-1) ...
279s Setting up r-cran-knitr (1.47+dfsg-1) ...
279s Setting up r-cran-mgcv (1.9-1-1) ...
279s Setting up r-cran-cachem (1.0.8-1) ...
279s Setting up r-cran-sass (0.4.9+dfsg-1) ...
279s Setting up r-cran-rcpparmadillo (14.0.0-1-1) ...
279s Setting up r-bioc-iranges (2.38.1-1) ...
279s Setting up r-cran-rjson (0.2.21-1) ...
279s Setting up r-cran-tzdb (0.4.0-2) ...
279s Setting up r-cran-argparse (2.2.3+dfsg-1) ...
279s Setting up r-cran-rcurl (1.98-1.14+dfsg-1build2) ...
279s Setting up r-cran-restfulr (0.0.15-1) ...
279s Setting up r-cran-vctrs (0.6.5-1) ...
279s Setting up r-cran-pillar (1.9.0+dfsg-1) ...
279s Setting up r-cran-ellipsis (0.3.2-2) ...
279s Setting up r-cran-openssl (2.2.0+dfsg-1) ...
279s Setting up r-bioc-s4arrays (1.4.1+dfsg-1) ...
279s Setting up r-cran-stringr (1.5.1-1) ...
279s Setting up r-bioc-biocparallel (1.38.0-2) ...
279s Setting up r-cran-callr (3.7.6-1) ...
279s Setting up r-cran-selectr (0.4-2-2build1) ...
279s Setting up r-bioc-edger (4.2.1+dfsg-1) ...
279s Setting up r-bioc-rhtslib (3.0.0+dfsg-1) ...
279s Setting up r-cran-xml2 (1.3.6-1) ...
279s Setting up r-cran-munsell (0.5.1-1) ...
279s Setting up r-cran-tibble (3.2.1+dfsg-2) ...
279s Setting up r-cran-fontawesome (0.5.2-1) ...
279s Setting up r-cran-survival (3.7-0-1) ...
279s Setting up r-bioc-biocio (1.14.0+dfsg-1) ...
279s Setting up r-cran-forcats (1.0.0-1) ...
279s Setting up r-cran-jquerylib (0.1.4+dfsg-4) ...
279s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ...
279s Setting up texlive-bibtex-extra (2024.20240706-2) ...
279s Setting up r-cran-reshape2 (1.4.4-2build1) ...
279s Setting up r-cran-httr2 (1.0.2-1) ...
279s Setting up r-cran-systemfonts (1.1.0-1) ...
279s Setting up r-cran-ids (1.0.1-2) ...
279s Setting up r-cran-timechange (0.3.0-1) ...
279s Setting up r-cran-httr (1.4.7+dfsg-1) ...
279s Setting up r-cran-gridextra (2.3-3build1) ...
279s Setting up r-cran-hms (1.1.3-1) ...
279s Setting up r-cran-scales (1.3.0-1) ...
279s Setting up r-cran-memoise (2.0.1-1) ...
279s Setting up r-cran-promises (1.3.0+dfsg-1) ...
279s Setting up r-cran-purrr (1.0.2-1) ...
279s Setting up r-cran-blob (1.2.4-1) ...
279s Setting up r-bioc-xvector (0.44.0-1) ...
279s Setting up r-cran-dplyr (1.1.4-1) ...
279s Setting up r-cran-rsqlite (2.3.7-2) ...
279s Setting up r-cran-progress (1.2.3-1) ...
279s Setting up r-cran-lubridate (1.9.3+dfsg-1) ...
279s Setting up r-cran-gargle (1.5.2-1) ...
279s Setting up r-cran-vroom (1.6.5-1) ...
279s Setting up r-cran-conflicted (1.2.0-1.1) ...
279s Setting up r-bioc-ucsc.utils (1.0.0+ds-2) ...
279s Setting up r-bioc-sparsearray (1.4.8+dfsg-1) ...
279s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ...
279s Setting up r-cran-cellranger (1.1.0-3) ...
279s Setting up r-cran-httpuv (1.6.15+dfsg-1) ...
279s Setting up r-cran-rematch2 (2.1.2-2build1) ...
279s Setting up r-cran-textshaping (0.3.7-2) ...
279s Setting up r-cran-rvest (1.0.4-1) ...
279s Setting up r-cran-dtplyr (1.3.1-1) ...
279s Setting up r-bioc-genomeinfodb (1.40.1+dfsg-1) ...
279s Setting up r-cran-bslib (0.7.0+dfsg-1) ...
279s Setting up r-cran-ragg (1.3.2-1) ...
279s Setting up r-cran-readr (2.1.5-1) ...
279s Setting up r-cran-tidyr (1.3.1-1) ...
279s Setting up r-cran-ggdendro (0.2.0+dfsg-1) ...
279s Setting up r-cran-googledrive (2.1.1-1) ...
279s Setting up r-cran-googlesheets4 (1.1.1-1) ...
279s Setting up r-bioc-qvalue (2.36.0-1) ...
279s Setting up r-cran-dbplyr (2.4.0+dfsg-1) ...
279s Setting up r-bioc-delayedarray (0.30.1+dfsg-1) ...
279s Setting up r-cran-readxl (1.4.3-1) ...
279s Setting up r-bioc-biocfilecache (2.12.0+dfsg-1) ...
279s Setting up r-cran-haven (2.5.4-1) ...
279s Setting up r-bioc-genomicranges (1.56.1+dfsg-1) ...
279s Setting up r-bioc-biostrings (2.72.1+dfsg-1) ...
279s Setting up r-cran-shiny (1.8.1.1+dfsg-1) ...
279s Setting up r-cran-broom (1.0.6+dfsg-1) ...
279s Setting up r-cran-rmarkdown (2.27+dfsg-1) ...
279s Setting up r-cran-goplot (1.0.2-2) ...
279s Setting up r-bioc-rsamtools (2.20.0+dfsg-1) ...
279s Setting up r-cran-bookdown (0.40+dfsg-1) ...
279s Setting up r-cran-reprex (2.1.0-1) ...
279s Setting up r-bioc-summarizedexperiment (1.34.0+dfsg-1) ...
279s Setting up r-bioc-keggrest (1.44.1+dfsg-1) ...
279s Setting up r-bioc-deseq2 (1.44.0+dfsg-1) ...
279s Setting up r-bioc-annotationdbi (1.66.0-1) ...
279s Setting up r-bioc-go.db (3.19.1-1) ...
279s Setting up r-cran-modelr (0.1.11-1) ...
279s Setting up r-bioc-annotate (1.82.0+dfsg-1) ...
279s Setting up r-bioc-biomart (2.60.1+dfsg-1) ...
279s Setting up r-bioc-genefilter (1.86.0-1) ...
279s Setting up r-bioc-biocstyle (2.32.1+dfsg-1) ...
279s Setting up r-bioc-genomicalignments (1.40.0-1) ...
279s Setting up r-bioc-geneplotter (1.82.0+dfsg-1) ...
279s Setting up r-bioc-rtracklayer (1.64.0-1) ...
279s Setting up r-bioc-genomicfeatures (1.56.0+dfsg-1) ...
279s Setting up r-cran-tidyverse (2.0.0+dfsg-1) ...
279s Setting up r-bioc-dexseq (1.50.0+dfsg-1) ...
279s Setting up r-bioc-txdbmaker (1.0.1+ds-1) ...
279s Setting up r-bioc-genelendatabase (1.40.1-1) ...
279s Setting up r-bioc-goseq (1.56.0-1) ...
279s Setting up adwaita-icon-theme (47.0-1) ...
279s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
279s Setting up liblwp-protocol-https-perl (6.14-1) ...
279s Setting up liberror-prone-java (2.18.0-1) ...
279s Setting up libwww-perl (6.77-1) ...
279s Setting up humanity-icon-theme (0.6.16) ...
279s Setting up libguava-java (32.0.1-1) ...
279s Setting up ubuntu-mono (24.04-0ubuntu1) ...
279s Setting up libjung-free-java (2.1.1-2) ...
279s Processing triggers for libglib2.0-0t64:arm64 (2.82.1-0ubuntu1) ...
279s Setting up libgtk-3-0t64:arm64 (3.24.43-3ubuntu2) ...
279s Processing triggers for install-info (7.1.1-1) ...
279s Processing triggers for libc-bin (2.40-1ubuntu3) ...
279s Processing triggers for man-db (2.12.1-3) ...
281s Processing triggers for ca-certificates-java (20240118) ...
281s Adding debian:ACCVRAIZ1.pem
281s Adding debian:AC_RAIZ_FNMT-RCM.pem
281s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
281s Adding debian:ANF_Secure_Server_Root_CA.pem
281s Adding debian:Actalis_Authentication_Root_CA.pem
281s Adding debian:AffirmTrust_Commercial.pem
281s Adding debian:AffirmTrust_Networking.pem
281s Adding debian:AffirmTrust_Premium.pem
281s Adding debian:AffirmTrust_Premium_ECC.pem
281s Adding debian:Amazon_Root_CA_1.pem
281s Adding debian:Amazon_Root_CA_2.pem
281s Adding debian:Amazon_Root_CA_3.pem
281s Adding debian:Amazon_Root_CA_4.pem
281s Adding debian:Atos_TrustedRoot_2011.pem
281s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
281s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
281s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
281s Adding debian:BJCA_Global_Root_CA1.pem
281s Adding debian:BJCA_Global_Root_CA2.pem
281s Adding debian:Baltimore_CyberTrust_Root.pem
281s Adding debian:Buypass_Class_2_Root_CA.pem
281s Adding debian:Buypass_Class_3_Root_CA.pem
281s Adding debian:CA_Disig_Root_R2.pem
281s Adding debian:CFCA_EV_ROOT.pem
281s Adding debian:COMODO_Certification_Authority.pem
281s Adding debian:COMODO_ECC_Certification_Authority.pem
281s Adding debian:COMODO_RSA_Certification_Authority.pem
281s Adding debian:Certainly_Root_E1.pem
281s Adding debian:Certainly_Root_R1.pem
281s Adding debian:Certigna.pem
281s Adding debian:Certigna_Root_CA.pem
281s Adding debian:Certum_EC-384_CA.pem
281s Adding debian:Certum_Trusted_Network_CA.pem
281s Adding debian:Certum_Trusted_Network_CA_2.pem
281s Adding debian:Certum_Trusted_Root_CA.pem
281s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
281s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
281s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
281s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
281s Adding debian:Comodo_AAA_Services_root.pem
281s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
281s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
281s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
281s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
281s Adding debian:DigiCert_Assured_ID_Root_CA.pem
281s Adding debian:DigiCert_Assured_ID_Root_G2.pem
281s Adding debian:DigiCert_Assured_ID_Root_G3.pem
281s Adding debian:DigiCert_Global_Root_CA.pem
281s Adding debian:DigiCert_Global_Root_G2.pem
281s Adding debian:DigiCert_Global_Root_G3.pem
281s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
281s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
281s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
281s Adding debian:DigiCert_Trusted_Root_G4.pem
281s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
281s Adding debian:Entrust_Root_Certification_Authority.pem
281s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
281s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
281s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
281s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
281s Adding debian:GLOBALTRUST_2020.pem
281s Adding debian:GTS_Root_R1.pem
281s Adding debian:GTS_Root_R2.pem
281s Adding debian:GTS_Root_R3.pem
281s Adding debian:GTS_Root_R4.pem
281s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
281s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
281s Adding debian:GlobalSign_Root_CA.pem
281s Adding debian:GlobalSign_Root_CA_-_R3.pem
281s Adding debian:GlobalSign_Root_CA_-_R6.pem
281s Adding debian:GlobalSign_Root_E46.pem
281s Adding debian:GlobalSign_Root_R46.pem
281s Adding debian:Go_Daddy_Class_2_CA.pem
282s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
282s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
282s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
282s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
282s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
282s Adding debian:HiPKI_Root_CA_-_G1.pem
282s Adding debian:Hongkong_Post_Root_CA_3.pem
282s Adding debian:ISRG_Root_X1.pem
282s Adding debian:ISRG_Root_X2.pem
282s Adding debian:IdenTrust_Commercial_Root_CA_1.pem
282s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
282s Adding debian:Izenpe.com.pem
282s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
282s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
282s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
282s Adding debian:NAVER_Global_Root_Certification_Authority.pem
282s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
282s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
282s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
282s Adding debian:QuoVadis_Root_CA_1_G3.pem
282s Adding debian:QuoVadis_Root_CA_2.pem
282s Adding debian:QuoVadis_Root_CA_2_G3.pem
282s Adding debian:QuoVadis_Root_CA_3.pem
282s Adding debian:QuoVadis_Root_CA_3_G3.pem
282s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
282s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
282s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
282s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
282s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
282s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
282s Adding debian:SZAFIR_ROOT_CA2.pem
282s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
282s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
282s Adding debian:SecureSign_RootCA11.pem
282s Adding debian:SecureTrust_CA.pem
282s Adding debian:Secure_Global_CA.pem
282s Adding debian:Security_Communication_ECC_RootCA1.pem
282s Adding debian:Security_Communication_RootCA2.pem
282s Adding debian:Security_Communication_RootCA3.pem
282s Adding debian:Security_Communication_Root_CA.pem
282s Adding debian:Starfield_Class_2_CA.pem
282s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
282s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
282s Adding debian:SwissSign_Gold_CA_-_G2.pem
282s Adding debian:SwissSign_Silver_CA_-_G2.pem
282s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
282s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
282s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
282s Adding debian:TWCA_Global_Root_CA.pem
282s Adding debian:TWCA_Root_Certification_Authority.pem
282s Adding debian:TeliaSonera_Root_CA_v1.pem
282s Adding debian:Telia_Root_CA_v2.pem
282s Adding debian:TrustAsia_Global_Root_CA_G3.pem
282s Adding debian:TrustAsia_Global_Root_CA_G4.pem
282s Adding debian:Trustwave_Global_Certification_Authority.pem
282s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
282s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
282s Adding debian:TunTrust_Root_CA.pem
282s Adding debian:UCA_Extended_Validation_Root.pem
282s Adding debian:UCA_Global_G2_Root.pem
282s Adding debian:USERTrust_ECC_Certification_Authority.pem
282s Adding debian:USERTrust_RSA_Certification_Authority.pem
282s Adding debian:XRamp_Global_CA_Root.pem
282s Adding debian:certSIGN_ROOT_CA.pem
282s Adding debian:certSIGN_Root_CA_G2.pem
282s Adding debian:e-Szigno_Root_CA_2017.pem
282s Adding debian:ePKI_Root_Certification_Authority.pem
282s Adding debian:emSign_ECC_Root_CA_-_C3.pem
282s Adding debian:emSign_ECC_Root_CA_-_G3.pem
282s Adding debian:emSign_Root_CA_-_C1.pem
282s Adding debian:emSign_Root_CA_-_G1.pem
282s Adding debian:vTrus_ECC_Root_CA.pem
282s Adding debian:vTrus_Root_CA.pem
282s done.
282s Setting up default-jre-headless (2:1.21-76) ...
282s Setting up jaligner (1.0+dfsg-11) ...
282s Setting up openjdk-21-jre:arm64 (21.0.5+11-1) ...
282s Setting up default-jre (2:1.21-76) ...
282s Setting up trimmomatic (0.39+dfsg-2) ...
282s Setting up trinityrnaseq (2.15.1+dfsg-5build1) ...
282s Setting up autopkgtest-satdep (0) ...
282s Processing triggers for tex-common (6.18) ...
282s Running updmap-sys. This may take some time... done.
282s Running mktexlsr /var/lib/texmf ... done.
282s Building format(s) --all.
319s 	This may take some time... done.
340s (Reading database ... 151644 files and directories currently installed.)
340s Removing autopkgtest-satdep (0) ...
341s autopkgtest [10:14:16]: test run-tests: [-----------------------
341s cd test_Trinity_Assembly && make test_all
341s make[1]: Entering directory '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly'
341s ./runMe.sh
341s #!/bin/bash -ve
341s 
341s #######################################################
341s ##  Run Trinity to Generate Transcriptome Assemblies ##
341s #######################################################
341s 
341s if [ -z ${TRINITY_HOME} ]; then
341s     echo "Must set env var TRINITY_HOME"
341s     exit 1
341s fi
341s 
341s 
341s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \
341s               --left reads.left.fq.gz \
341s               --right reads.right.fq.gz \
341s               --SS_lib_type RF \
341s               --CPU 1 \
341s               --no_cleanup
341s 
341s 
341s      ______  ____   ____  ____   ____  ______  __ __
341s     |      ||    \ |    ||    \ |    ||      ||  |  |
341s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
341s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
341s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
341s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
341s       |__|  |__|\_||____||__|__||____|  |__|  |____/
341s 
341s     Trinity-v2.15.1
341s 
341s 
341s 
341s Left read files: $VAR1 = [
341s           'reads.left.fq.gz'
341s         ];
341s Right read files: $VAR1 = [
341s           'reads.right.fq.gz'
341s         ];
341s Friday, November 1, 2024: 10:14:16	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir
341s Friday, November 1, 2024: 10:14:16	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis
341s 
341s 
341s ----------------------------------------------------------------------------------
341s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
341s ----------------------------------------------------------------------------------
341s 
341s ---------------------------------------------------------------
341s ------------ In silico Read Normalization ---------------------
341s -- (Removing Excess Reads Beyond 200 Coverage --
341s ---------------------------------------------------------------
341s 
341s # running normalization on reads: $VAR1 = [
341s           [
341s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
341s           ],
341s           [
341s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
341s           ]
341s         ];
341s 
341s 
341s Friday, November 1, 2024: 10:14:16	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 1 --output /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together  --PARALLEL_STATS  
341s -prepping seqs
341s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
341s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
341s CMD finished (0 seconds)
341s CMD finished (0 seconds)
341s CMD: touch left.fa.ok
341s CMD finished (0 seconds)
341s CMD: touch right.fa.ok
341s CMD finished (0 seconds)
341s Done converting input files.CMD: cat left.fa right.fa > both.fa
342s CMD finished (0 seconds)
342s CMD: touch both.fa.ok
342s CMD finished (0 seconds)
342s -kmer counting.
342s -------------------------------------------
342s ----------- Jellyfish  --------------------
342s -- (building a k-mer catalog from reads) --
342s -------------------------------------------
342s 
342s CMD: jellyfish count -t 1 -m 25 -s 100000000  both.fa
344s CMD finished (3 seconds)
344s CMD: jellyfish histo -t 1 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
344s CMD finished (0 seconds)
344s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
344s CMD finished (0 seconds)
344s CMD: touch jellyfish.K25.min2.kmers.fa.success
344s CMD finished (0 seconds)
344s -generating stats files
344s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
344s -reading Kmer occurrences...
344s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
344s -reading Kmer occurrences...
344s 
344s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
344s 
344s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
345s STATS_GENERATION_TIME: 1 seconds.
345s STATS_GENERATION_TIME: 1 seconds.
345s CMD finished (1 seconds)
345s CMD finished (1 seconds)
345s CMD: touch left.fa.K25.stats.ok
345s CMD finished (0 seconds)
345s CMD: touch right.fa.K25.stats.ok
345s CMD finished (0 seconds)
345s -sorting each stats file by read name.
345s 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
345s 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
345s CMD finished (0 seconds)
345s CMD finished (0 seconds)
345s CMD: touch left.fa.K25.stats.sort.ok
345s CMD finished (0 seconds)
345s CMD: touch right.fa.K25.stats.sort.ok
345s CMD finished (0 seconds)
345s -defining normalized reads
345s 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
345s -opening left.fa.K25.stats.sort
345s -opening right.fa.K25.stats.sort
345s -done opening files.
345s CMD finished (0 seconds)
345s CMD: touch pairs.K25.stats.ok
345s CMD finished (0 seconds)
345s 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
346s 30472 / 30575 = 99.66% reads selected during normalization.
346s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
346s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
346s CMD finished (1 seconds)
346s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
346s CMD finished (0 seconds)
346s -search and capture.
346s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture.
346s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
346s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture.
346s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
346s CMD: touch /tmp/autopkgtest.xkSdGF/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
346s CMD finished (0 seconds)
346s CMD: touch /tmp/autopkgtest.xkSdGF/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
346s CMD finished (0 seconds)
346s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
346s CMD finished (0 seconds)
346s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
346s CMD finished (0 seconds)
346s 
346s 
346s Normalization complete. See outputs: 
346s 	/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
346s 	/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
346s Friday, November 1, 2024: 10:14:21	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/insilico_read_normalization/normalization.ok
346s Converting input files. (in parallel)Friday, November 1, 2024: 10:14:21	CMD: cat /tmp/autopkgtest.xkSdGF/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
346s Friday, November 1, 2024: 10:14:21	CMD: cat /tmp/autopkgtest.xkSdGF/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
346s Friday, November 1, 2024: 10:14:21	CMD: touch left.fa.ok
346s Friday, November 1, 2024: 10:14:21	CMD: touch right.fa.ok
346s Friday, November 1, 2024: 10:14:21	CMD: touch left.fa.ok right.fa.ok
346s Friday, November 1, 2024: 10:14:21	CMD: cat left.fa right.fa > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
346s Friday, November 1, 2024: 10:14:21	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa.ok
346s -------------------------------------------
346s ----------- Jellyfish  --------------------
346s -- (building a k-mer (25) catalog from reads) --
346s -------------------------------------------
346s 
346s * [Fri Nov  1 10:14:21 2024] Running CMD: jellyfish count -t 1 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
349s * [Fri Nov  1 10:14:24 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
349s * [Fri Nov  1 10:14:24 2024] Running CMD: jellyfish histo -t 1 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
349s ----------------------------------------------
349s --------------- Inchworm (K=25, asm) ---------------------
349s -- (Linear contig construction from k-mers) --
349s ----------------------------------------------
349s 
349s * [Fri Nov  1 10:14:24 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa.tmp
349s Kmer length set to: 25
349s Min assembly length set to: 25
349s Monitor turned on, set to: 1
349s -retaining tmp files
349s min entropy set to: 1
349s setting number of threads to: 1
349s -setting parallel iworm mode.
349s -reading Kmer occurrences...
349s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
349s  done parsing 519541 Kmers, 519541 added, taking 0 seconds.
349s 
349s TIMING KMER_DB_BUILDING 0 s.
350s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
350s Pruned 4252 kmers from catalog.
350s 	Pruning time: 1 seconds = 0.0166667 minutes.
350s 
350s TIMING PRUNING 1 s.
350s -populating the kmer seed candidate list.
350s Kcounter hash size: 519541
350s Processed 515289 non-zero abundance kmers in kcounter.
350s -Not sorting list of kmers, given parallel mode in effect.
350s -beginning inchworm contig assembly.
350s Total kcounter hash size: 519541 vs. sorted list size: 515289
350s num threads set to: 1
350s Done opening file. tmp.iworm.fa.pid_8456.thread_0
350s 
350s 	Iworm contig assembly time: 0 seconds = 0 minutes.
350s 
350s TIMING CONTIG_BUILDING 0 s.
350s 
350s TIMING PROG_RUNTIME 1 s.
350s * [Fri Nov  1 10:14:25 2024] Running CMD: mv /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa.tmp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa
350s Friday, November 1, 2024: 10:14:25	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa.finished
350s --------------------------------------------------------
350s -------------------- Chrysalis -------------------------
350s -- (Contig Clustering & de Bruijn Graph Construction) --
350s --------------------------------------------------------
350s 
350s inchworm_target: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
350s bowtie_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
350s chrysalis_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa
350s * [Fri Nov  1 10:14:25 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.fa 100 10 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100
351s * [Fri Nov  1 10:14:25 2024] Running CMD: /usr/bin/bowtie2-build --threads 1 -o 3 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 1>/dev/null
351s * [Fri Nov  1 10:14:26 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" 
354s * [Fri Nov  1 10:14:29 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_scaffolds.txt
354s * [Fri Nov  1 10:14:29 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt
355s * [Fri Nov  1 10:14:30 2024] Running CMD: /usr/bin/sort --parallel=1 -T . -S 2G  -k9,9gr /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted
355s * [Fri Nov  1 10:14:30 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
355s * [Fri Nov  1 10:14:30 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/GraphFromIwormFasta.out
355s * [Fri Nov  1 10:14:30 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200
355s * [Fri Nov  1 10:14:30 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa -f /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/readsToComponents.out -t 1 -max_mem_reads 50000000  -strand  -p 10 
359s * [Fri Nov  1 10:14:34 2024] Running CMD: /usr/bin/sort --parallel=1 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/readsToComponents.out > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/readsToComponents.out.sort
359s Friday, November 1, 2024: 10:14:34	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/read_partitions/Fb_0/CBin_0
359s Friday, November 1, 2024: 10:14:34	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/partitioned_reads.files.list.ok
359s Friday, November 1, 2024: 10:14:34	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.xkSdGF/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
360s Friday, November 1, 2024: 10:14:34	CMD: touch recursive_trinity.cmds.ok
360s Friday, November 1, 2024: 10:14:34	CMD: touch recursive_trinity.cmds.ok
360s 
360s 
360s --------------------------------------------------------------------------------
360s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
360s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
360s --------------------------------------------------------------------------------
360s 
360s Friday, November 1, 2024: 10:14:34	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 1 -v -shuffle 
360s Number of Commands: 36
444s 
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.    
444s 
444s All commands completed successfully. :-)
444s 
444s 
444s 
444s ** Harvesting all assembled transcripts into a single multi-fasta file...
444s 
444s Friday, November 1, 2024: 10:15:59	CMD: find /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/Trinity.tmp
444s * [Fri Nov  1 10:15:59 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa 1
445s * [Fri Nov  1 10:16:00 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta
445s Friday, November 1, 2024: 10:16:00	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta.gene_trans_map
445s 
445s 
445s #############################################################################
445s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_out_dir.Trinity.fasta
445s #############################################################################
445s 
445s 
445s ./misc_run_tests/__test_runMe_NO_normalization.sh
445s 
445s ##### Done Running Trinity #####
445s 
445s if [ $* ]; then
445s     # check full-length reconstruction stats:
445s 
445s     ${TRINITY_HOME}/util/misc/illustrate_ref_comparison.pl __indiv_ex_sample_derived/refSeqs.fa trinity_out_dir.Trinity.fasta 90
445s 
445s     ./test_FL.sh --query  trinity_out_dir.Trinity.fasta --target __indiv_ex_sample_derived/refSeqs.fa --no_reuse
445s 
445s fi
445s 
445s #!/bin/bash -ve
445s 
445s 
445s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
445s     gunzip -c reads.right.fq.gz > reads.right.fq
445s fi
445s 
445s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
445s     gunzip -c reads.left.fq.gz > reads.left.fq
445s fi
445s 
445s 
445s 
445s #######################################################
445s ##  Run Trinity to Generate Transcriptome Assemblies ##
445s #######################################################
445s 
445s CPU=$(nproc || sysctl -n hw.physicalcpu)
445s 
445s ## use jellyfish
445s ${TRINITY_HOME}/Trinity --seqType fq \
445s               --max_memory 2G \
445s               --left reads.left.fq \
445s               --right reads.right.fq \
445s               --SS_lib_type RF \
445s               --CPU ${CPU} \
445s               --no_normalize_reads \
445s               --output __test_trinity_wo_normalization
445s 
445s 
445s      ______  ____   ____  ____   ____  ______  __ __
445s     |      ||    \ |    ||    \ |    ||      ||  |  |
445s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
445s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
445s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
445s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
445s       |__|  |__|\_||____||__|__||____|  |__|  |____/
445s 
445s     Trinity-v2.15.1
445s 
445s 
445s 
445s Left read files: $VAR1 = [
445s           'reads.left.fq'
445s         ];
445s Right read files: $VAR1 = [
445s           'reads.right.fq'
445s         ];
445s Friday, November 1, 2024: 10:16:00	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization
445s Friday, November 1, 2024: 10:16:00	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis
445s 
445s 
445s ----------------------------------------------------------------------------------
445s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
445s ----------------------------------------------------------------------------------
445s 
445s Converting input files. (in parallel)Friday, November 1, 2024: 10:16:00	CMD: cat /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa
445s Friday, November 1, 2024: 10:16:00	CMD: cat /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq | seqtk-trinity seq -A -R 2 - >> right.fa
445s Friday, November 1, 2024: 10:16:00	CMD: touch left.fa.ok
445s Friday, November 1, 2024: 10:16:00	CMD: touch right.fa.ok
445s Friday, November 1, 2024: 10:16:00	CMD: touch left.fa.ok right.fa.ok
445s Friday, November 1, 2024: 10:16:00	CMD: cat left.fa right.fa > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
445s Friday, November 1, 2024: 10:16:00	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa.ok
445s -------------------------------------------
445s ----------- Jellyfish  --------------------
445s -- (building a k-mer (25) catalog from reads) --
445s -------------------------------------------
445s 
445s * [Fri Nov  1 10:16:00 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
447s * [Fri Nov  1 10:16:02 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
447s * [Fri Nov  1 10:16:02 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
447s ----------------------------------------------
447s --------------- Inchworm (K=25, asm) ---------------------
447s -- (Linear contig construction from k-mers) --
447s ----------------------------------------------
447s 
447s * [Fri Nov  1 10:16:02 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa.tmp
447s Kmer length set to: 25
447s Min assembly length set to: 25
447s Monitor turned on, set to: 1
447s min entropy set to: 1
447s setting number of threads to: 2
447s -setting parallel iworm mode.
447s -reading Kmer occurrences...
447s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
447s  done parsing 520108 Kmers, 520108 added, taking 0 seconds.
447s 
447s TIMING KMER_DB_BUILDING 0 s.
447s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
447s Pruned 4291 kmers from catalog.
447s 	Pruning time: 0 seconds = 0 minutes.
447s 
447s TIMING PRUNING 0 s.
447s -populating the kmer seed candidate list.
447s Kcounter hash size: 520108
448s Processed 515817 non-zero abundance kmers in kcounter.
448s -Not sorting list of kmers, given parallel mode in effect.
448s -beginning inchworm contig assembly.
448s Total kcounter hash size: 520108 vs. sorted list size: 515817
448s num threads set to: 2
448s Done opening file. tmp.iworm.fa.pid_14733.thread_0
448s Done opening file. tmp.iworm.fa.pid_14733.thread_1
448s 
448s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
448s 
448s TIMING CONTIG_BUILDING 1 s.
448s 
448s TIMING PROG_RUNTIME 1 s.
448s * [Fri Nov  1 10:16:03 2024] Running CMD: mv /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa.tmp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa
448s Friday, November 1, 2024: 10:16:03	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa.finished
448s --------------------------------------------------------
448s -------------------- Chrysalis -------------------------
448s -- (Contig Clustering & de Bruijn Graph Construction) --
448s --------------------------------------------------------
448s 
448s inchworm_target: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
448s bowtie_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
448s chrysalis_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa
448s * [Fri Nov  1 10:16:03 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/inchworm.fa 100 10 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100
448s * [Fri Nov  1 10:16:03 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 1>/dev/null
448s * [Fri Nov  1 10:16:03 2024] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm.bowtie.nameSorted.bam" 
451s * [Fri Nov  1 10:16:06 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_scaffolds.txt
452s * [Fri Nov  1 10:16:07 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt
453s * [Fri Nov  1 10:16:08 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted
453s * [Fri Nov  1 10:16:08 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
453s * [Fri Nov  1 10:16:08 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/GraphFromIwormFasta.out
453s * [Fri Nov  1 10:16:08 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/bundled_iworm_contigs.fasta -min 200
453s * [Fri Nov  1 10:16:08 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa -f /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -strand  -p 10 
455s * [Fri Nov  1 10:16:10 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/readsToComponents.out > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/chrysalis/readsToComponents.out.sort
455s Friday, November 1, 2024: 10:16:10	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/read_partitions/Fb_0/CBin_0
456s Friday, November 1, 2024: 10:16:11	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/partitioned_reads.files.list.ok
456s Friday, November 1, 2024: 10:16:11	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.xkSdGF/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
456s Friday, November 1, 2024: 10:16:11	CMD: touch recursive_trinity.cmds.ok
456s Friday, November 1, 2024: 10:16:11	CMD: touch recursive_trinity.cmds.ok
456s 
456s 
456s --------------------------------------------------------------------------------
456s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
456s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
456s --------------------------------------------------------------------------------
456s 
456s Friday, November 1, 2024: 10:16:11	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
456s Number of Commands: 38
521s 
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.    
521s 
521s All commands completed successfully. :-)
521s 
521s 
521s 
521s ** Harvesting all assembled transcripts into a single multi-fasta file...
521s 
521s Friday, November 1, 2024: 10:17:16	CMD: find /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/Trinity.tmp
521s * [Fri Nov  1 10:17:16 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa 2
522s * [Fri Nov  1 10:17:17 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta
522s Friday, November 1, 2024: 10:17:17	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta.gene_trans_map
522s 
522s 
522s #############################################################################
522s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_wo_normalization.Trinity.fasta
522s #############################################################################
522s 
522s 
522s ./misc_run_tests/__runMe_with_qual_trimming.sh
522s 
522s 
522s 
522s #!/bin/bash -ve
522s 
522s 
522s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
522s     gunzip -c reads.right.fq.gz > reads.right.fq
522s fi
522s 
522s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
522s     gunzip -c reads.left.fq.gz > reads.left.fq
522s fi
522s 
522s 
522s 
522s #######################################################
522s ##  Run Trinity to Generate Transcriptome Assemblies ##
522s #######################################################
522s 
522s CPU=$(nproc || sysctl -n hw.physicalcpu)
522s 
522s ${TRINITY_HOME}/Trinity \
522s     --seqType fq \
522s     --max_memory 2G \
522s     --left reads.left.fq \
522s     --right reads.right.fq \
522s     --SS_lib_type RF \
522s     --CPU ${CPU} \
522s     --no_normalize_reads \
522s     --trimmomatic \
522s     --output __test_trinity_with_trimmomatic
522s 
522s 
522s      ______  ____   ____  ____   ____  ______  __ __
522s     |      ||    \ |    ||    \ |    ||      ||  |  |
522s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
522s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
522s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
522s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
522s       |__|  |__|\_||____||__|__||____|  |__|  |____/
522s 
522s     Trinity-v2.15.1
522s 
522s 
522s 
522s Left read files: $VAR1 = [
522s           'reads.left.fq'
522s         ];
522s Right read files: $VAR1 = [
522s           'reads.right.fq'
522s         ];
522s Friday, November 1, 2024: 10:17:17	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic
522s Friday, November 1, 2024: 10:17:17	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis
522s 
522s 
522s ----------------------------------------------------------------------------------
522s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
522s ----------------------------------------------------------------------------------
522s 
522s ---------------------------------------------------------------
522s ------ Quality Trimming Via Trimmomatic  ---------------------
522s << ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >>
522s ---------------------------------------------------------------
522s 
522s 
522s ## Running Trimmomatic on read files: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq, /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq
522s Friday, November 1, 2024: 10:17:17	CMD: java  -jar /usr/share/java/trimmomatic.jar PE -threads 2  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.xkSdGF/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 
522s TrimmomaticPE: Started with arguments:
522s  -threads 2 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.xkSdGF/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
522s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
522s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
522s Quality encoding detected as phred33
523s 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%)
523s TrimmomaticPE: Completed successfully
523s Friday, November 1, 2024: 10:17:18	CMD: cat reads.left.fq.P.qtrim reads.left.fq.U.qtrim > reads.left.fq.PwU.qtrim.fq
523s Friday, November 1, 2024: 10:17:18	CMD: cat reads.right.fq.P.qtrim reads.right.fq.U.qtrim > reads.right.fq.PwU.qtrim.fq
523s Friday, November 1, 2024: 10:17:18	CMD: touch trimmomatic.ok
523s Friday, November 1, 2024: 10:17:18	CMD: gzip reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim &
523s Converting input files. (in parallel)Friday, November 1, 2024: 10:17:18	CMD: cat reads.left.fq.PwU.qtrim.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa
523s Friday, November 1, 2024: 10:17:18	CMD: cat reads.right.fq.PwU.qtrim.fq | seqtk-trinity seq -A -R 2 - >> right.fa
523s Friday, November 1, 2024: 10:17:18	CMD: touch left.fa.ok
523s Friday, November 1, 2024: 10:17:18	CMD: touch right.fa.ok
523s Friday, November 1, 2024: 10:17:18	CMD: touch left.fa.ok right.fa.ok
523s Friday, November 1, 2024: 10:17:18	CMD: cat left.fa right.fa > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
523s Friday, November 1, 2024: 10:17:18	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa.ok
523s -------------------------------------------
523s ----------- Jellyfish  --------------------
523s -- (building a k-mer (25) catalog from reads) --
523s -------------------------------------------
523s 
523s * [Fri Nov  1 10:17:18 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
524s * [Fri Nov  1 10:17:19 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
525s * [Fri Nov  1 10:17:19 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
525s ----------------------------------------------
525s --------------- Inchworm (K=25, asm) ---------------------
525s -- (Linear contig construction from k-mers) --
525s ----------------------------------------------
525s 
525s * [Fri Nov  1 10:17:20 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa.tmp
525s Kmer length set to: 25
525s Min assembly length set to: 25
525s Monitor turned on, set to: 1
525s min entropy set to: 1
525s setting number of threads to: 2
525s -setting parallel iworm mode.
525s -reading Kmer occurrences...
525s 
 [0M] Kmers parsed.     
525s  done parsing 318541 Kmers, 318541 added, taking 0 seconds.
525s 
525s TIMING KMER_DB_BUILDING 0 s.
525s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
525s Pruned 1498 kmers from catalog.
525s 	Pruning time: 0 seconds = 0 minutes.
525s 
525s TIMING PRUNING 0 s.
525s -populating the kmer seed candidate list.
525s Kcounter hash size: 318541
525s Processed 317043 non-zero abundance kmers in kcounter.
525s -Not sorting list of kmers, given parallel mode in effect.
525s -beginning inchworm contig assembly.
525s Total kcounter hash size: 318541 vs. sorted list size: 317043
525s num threads set to: 2
525s Done opening file. tmp.iworm.fa.pid_21479.thread_0
525s Done opening file. tmp.iworm.fa.pid_21479.thread_1
525s 
525s 	Iworm contig assembly time: 0 seconds = 0 minutes.
525s 
525s TIMING CONTIG_BUILDING 0 s.
525s 
525s TIMING PROG_RUNTIME 0 s.
525s * [Fri Nov  1 10:17:20 2024] Running CMD: mv /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa.tmp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa
525s Friday, November 1, 2024: 10:17:20	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa.finished
525s --------------------------------------------------------
525s -------------------- Chrysalis -------------------------
525s -- (Contig Clustering & de Bruijn Graph Construction) --
525s --------------------------------------------------------
525s 
525s inchworm_target: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
525s bowtie_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
525s chrysalis_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa
525s * [Fri Nov  1 10:17:20 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/inchworm.fa 100 10 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100
525s * [Fri Nov  1 10:17:20 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 1>/dev/null
526s * [Fri Nov  1 10:17:21 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm.bowtie.nameSorted.bam" 
528s * [Fri Nov  1 10:17:23 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_scaffolds.txt
529s * [Fri Nov  1 10:17:24 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt
532s * [Fri Nov  1 10:17:27 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted
532s * [Fri Nov  1 10:17:27 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
532s * [Fri Nov  1 10:17:27 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/GraphFromIwormFasta.out
532s * [Fri Nov  1 10:17:27 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/bundled_iworm_contigs.fasta -min 200
532s * [Fri Nov  1 10:17:27 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa -f /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -strand  -p 10 
533s * [Fri Nov  1 10:17:28 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/readsToComponents.out > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/chrysalis/readsToComponents.out.sort
534s Friday, November 1, 2024: 10:17:29	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/read_partitions/Fb_0/CBin_0
534s Friday, November 1, 2024: 10:17:29	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/partitioned_reads.files.list.ok
534s Friday, November 1, 2024: 10:17:29	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.xkSdGF/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
534s Friday, November 1, 2024: 10:17:29	CMD: touch recursive_trinity.cmds.ok
534s Friday, November 1, 2024: 10:17:29	CMD: touch recursive_trinity.cmds.ok
534s 
534s 
534s --------------------------------------------------------------------------------
534s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
534s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
534s --------------------------------------------------------------------------------
534s 
534s Friday, November 1, 2024: 10:17:29	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
534s Number of Commands: 35
593s 
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.    
593s 
593s All commands completed successfully. :-)
593s 
593s 
593s 
593s ** Harvesting all assembled transcripts into a single multi-fasta file...
593s 
593s Friday, November 1, 2024: 10:18:28	CMD: find /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/Trinity.tmp
593s * [Fri Nov  1 10:18:28 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa 2
594s * [Fri Nov  1 10:18:29 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta
594s Friday, November 1, 2024: 10:18:29	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta.gene_trans_map
594s 
594s 
594s #############################################################################
594s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_with_trimmomatic.Trinity.fasta
594s #############################################################################
594s 
594s 
594s 
594s ##### Done Running Trinity #####
594s 
594s ./misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh
594s #!/bin/bash -ve
594s 
594s 
594s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
594s     gunzip -c reads.right.fq.gz > reads.right.fq
594s fi
594s 
594s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
594s     gunzip -c reads.left.fq.gz > reads.left.fq
594s fi
594s 
594s 
594s 
594s #######################################################
594s ##  Run Trinity to Generate Transcriptome Assemblies ##
594s #######################################################
594s 
594s CPU=$(nproc || sysctl -n hw.physicalcpu)
594s 
594s ${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
594s 
594s 
594s      ______  ____   ____  ____   ____  ______  __ __
594s     |      ||    \ |    ||    \ |    ||      ||  |  |
594s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
594s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
594s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
594s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
594s       |__|  |__|\_||____||__|__||____|  |__|  |____/
594s 
594s     Trinity-v2.15.1
594s 
594s 
594s 
594s Left read files: $VAR1 = [
594s           'reads.left.fq'
594s         ];
594s Right read files: $VAR1 = [
594s           'reads.right.fq'
594s         ];
594s Friday, November 1, 2024: 10:18:29	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm
594s Friday, November 1, 2024: 10:18:29	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis
594s 
594s 
594s ----------------------------------------------------------------------------------
594s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
594s ----------------------------------------------------------------------------------
594s 
594s ---------------------------------------------------------------
594s ------ Quality Trimming Via Trimmomatic  ---------------------
594s << ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >>
594s ---------------------------------------------------------------
594s 
594s 
594s ## Running Trimmomatic on read files: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq, /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq
594s Friday, November 1, 2024: 10:18:29	CMD: java  -jar /usr/share/java/trimmomatic.jar PE -threads 2  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.xkSdGF/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 
594s TrimmomaticPE: Started with arguments:
594s  -threads 2 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.xkSdGF/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
594s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
594s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
594s Quality encoding detected as phred33
595s 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%)
595s TrimmomaticPE: Completed successfully
595s Friday, November 1, 2024: 10:18:30	CMD: cp reads.left.fq.P.qtrim reads.left.fq.PwU.qtrim.fq
595s Friday, November 1, 2024: 10:18:30	CMD: cp reads.right.fq.P.qtrim reads.right.fq.PwU.qtrim.fq
595s Friday, November 1, 2024: 10:18:30	CMD: touch trimmomatic.ok
595s Friday, November 1, 2024: 10:18:30	CMD: gzip reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim &
595s ---------------------------------------------------------------
595s ------------ In silico Read Normalization ---------------------
595s -- (Removing Excess Reads Beyond 200 Coverage --
595s ---------------------------------------------------------------
595s 
595s # running normalization on reads: $VAR1 = [
595s           [
595s             'reads.left.fq.PwU.qtrim.fq'
595s           ],
595s           [
595s             'reads.right.fq.PwU.qtrim.fq'
595s           ]
595s         ];
595s 
595s 
595s Friday, November 1, 2024: 10:18:30	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.xkSdGF/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  
595s -prepping seqs
595s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.left.fq.PwU.qtrim.fq >> left.fa
595s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.right.fq.PwU.qtrim.fq >> right.fa
595s CMD finished (0 seconds)
595s CMD finished (0 seconds)
595s CMD: touch left.fa.ok
595s CMD finished (0 seconds)
595s CMD: touch right.fa.ok
595s CMD finished (0 seconds)
595s Done converting input files.CMD: cat left.fa right.fa > both.fa
595s CMD finished (0 seconds)
595s CMD: touch both.fa.ok
595s CMD finished (0 seconds)
595s -kmer counting.
595s -------------------------------------------
595s ----------- Jellyfish  --------------------
595s -- (building a k-mer catalog from reads) --
595s -------------------------------------------
595s 
595s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
597s CMD finished (2 seconds)
597s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
597s CMD finished (0 seconds)
597s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
597s CMD finished (0 seconds)
597s CMD: touch jellyfish.K25.min2.kmers.fa.success
597s CMD finished (0 seconds)
597s -generating stats files
597s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
597s -reading Kmer occurrences...
597s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
597s -reading Kmer occurrences...
597s 
597s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
597s 
597s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
597s STATS_GENERATION_TIME: 0 seconds.
597s CMD finished (0 seconds)
597s STATS_GENERATION_TIME: 0 seconds.
597s CMD finished (0 seconds)
597s CMD: touch left.fa.K25.stats.ok
597s CMD finished (0 seconds)
597s CMD: touch right.fa.K25.stats.ok
597s CMD finished (0 seconds)
597s -sorting each stats file by read name.
597s 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
597s 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
597s CMD finished (0 seconds)
597s CMD finished (0 seconds)
597s CMD: touch left.fa.K25.stats.sort.ok
597s CMD finished (0 seconds)
597s CMD: touch right.fa.K25.stats.sort.ok
597s CMD finished (0 seconds)
597s -defining normalized reads
597s 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
597s -opening left.fa.K25.stats.sort
597s -opening right.fa.K25.stats.sort
597s -done opening files.
598s CMD finished (1 seconds)
598s CMD: touch pairs.K25.stats.ok
598s CMD finished (0 seconds)
598s 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
598s 27678 / 27726 = 99.83% reads selected during normalization.
598s 0 / 27726 = 0.00% reads discarded as likely aberrant based on coverage profiles.
598s 0 / 27726 = 0.00% reads discarded as below minimum coverage threshold=1
598s CMD finished (0 seconds)
598s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
598s CMD finished (0 seconds)
598s -search and capture.
599s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/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.
599s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.left.fq.PwU.qtrim.fq
599s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/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.
599s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/reads.right.fq.PwU.qtrim.fq
599s CMD: touch /tmp/autopkgtest.xkSdGF/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
599s CMD finished (0 seconds)
599s CMD: touch /tmp/autopkgtest.xkSdGF/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
599s CMD finished (0 seconds)
599s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
599s CMD finished (0 seconds)
599s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
599s CMD finished (0 seconds)
599s -removing tmp dir /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/tmp_normalized_reads
599s 
599s 
599s Normalization complete. See outputs: 
599s 	/tmp/autopkgtest.xkSdGF/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
599s 	/tmp/autopkgtest.xkSdGF/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
599s Friday, November 1, 2024: 10:18:34	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/insilico_read_normalization/normalization.ok
599s Converting input files. (in parallel)Friday, November 1, 2024: 10:18:34	CMD: cat /tmp/autopkgtest.xkSdGF/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
599s Friday, November 1, 2024: 10:18:34	CMD: cat /tmp/autopkgtest.xkSdGF/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
599s Friday, November 1, 2024: 10:18:34	CMD: touch right.fa.ok
599s Friday, November 1, 2024: 10:18:34	CMD: touch left.fa.ok
599s Friday, November 1, 2024: 10:18:34	CMD: touch left.fa.ok right.fa.ok
599s Friday, November 1, 2024: 10:18:34	CMD: cat left.fa right.fa > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
599s Friday, November 1, 2024: 10:18:34	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa.ok
599s -------------------------------------------
599s ----------- Jellyfish  --------------------
599s -- (building a k-mer (25) catalog from reads) --
599s -------------------------------------------
599s 
599s * [Fri Nov  1 10:18:34 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
600s * [Fri Nov  1 10:18:35 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
600s * [Fri Nov  1 10:18:35 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
600s ----------------------------------------------
600s --------------- Inchworm (K=25, asm) ---------------------
600s -- (Linear contig construction from k-mers) --
600s ----------------------------------------------
600s 
600s * [Fri Nov  1 10:18:35 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa.tmp
600s Kmer length set to: 25
600s Min assembly length set to: 25
600s Monitor turned on, set to: 1
600s min entropy set to: 1
600s setting number of threads to: 2
600s -setting parallel iworm mode.
600s -reading Kmer occurrences...
601s 
 [0M] Kmers parsed.     
601s  done parsing 311705 Kmers, 311705 added, taking 0 seconds.
601s 
601s TIMING KMER_DB_BUILDING 0 s.
601s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
601s Pruned 1486 kmers from catalog.
601s 	Pruning time: 1 seconds = 0.0166667 minutes.
601s 
601s TIMING PRUNING 1 s.
601s -populating the kmer seed candidate list.
601s Kcounter hash size: 311705
601s Processed 310219 non-zero abundance kmers in kcounter.
601s -Not sorting list of kmers, given parallel mode in effect.
601s -beginning inchworm contig assembly.
601s Total kcounter hash size: 311705 vs. sorted list size: 310219
601s num threads set to: 2
601s Done opening file. tmp.iworm.fa.pid_27770.thread_0
601s Done opening file. tmp.iworm.fa.pid_27770.thread_1
601s 
601s 	Iworm contig assembly time: 0 seconds = 0 minutes.
601s 
601s TIMING CONTIG_BUILDING 0 s.
601s 
601s TIMING PROG_RUNTIME 1 s.
601s * [Fri Nov  1 10:18:36 2024] Running CMD: mv /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa.tmp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa
601s Friday, November 1, 2024: 10:18:36	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa.finished
601s --------------------------------------------------------
601s -------------------- Chrysalis -------------------------
601s -- (Contig Clustering & de Bruijn Graph Construction) --
601s --------------------------------------------------------
601s 
601s inchworm_target: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
601s bowtie_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
601s chrysalis_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa
601s * [Fri Nov  1 10:18:36 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/inchworm.fa 100 10 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100
601s * [Fri Nov  1 10:18:36 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 1>/dev/null
601s * [Fri Nov  1 10:18:36 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm.bowtie.nameSorted.bam" 
604s * [Fri Nov  1 10:18:39 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_scaffolds.txt
605s * [Fri Nov  1 10:18:40 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt
607s * [Fri Nov  1 10:18:42 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted
607s * [Fri Nov  1 10:18:42 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
607s * [Fri Nov  1 10:18:42 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/GraphFromIwormFasta.out
607s * [Fri Nov  1 10:18:42 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/bundled_iworm_contigs.fasta -min 200
607s * [Fri Nov  1 10:18:42 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa -f /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.xkSdGF/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 
609s * [Fri Nov  1 10:18:44 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/readsToComponents.out > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/chrysalis/readsToComponents.out.sort
609s Friday, November 1, 2024: 10:18:44	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/read_partitions/Fb_0/CBin_0
610s Friday, November 1, 2024: 10:18:44	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/partitioned_reads.files.list.ok
610s Friday, November 1, 2024: 10:18:44	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.xkSdGF/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
610s Friday, November 1, 2024: 10:18:45	CMD: touch recursive_trinity.cmds.ok
610s Friday, November 1, 2024: 10:18:45	CMD: touch recursive_trinity.cmds.ok
610s 
610s 
610s --------------------------------------------------------------------------------
610s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
610s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
610s --------------------------------------------------------------------------------
610s 
610s Friday, November 1, 2024: 10:18:45	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
610s Number of Commands: 38
668s 
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.    
668s 
668s All commands completed successfully. :-)
668s 
668s 
668s 
668s ** Harvesting all assembled transcripts into a single multi-fasta file...
668s 
668s Friday, November 1, 2024: 10:19:43	CMD: find /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/Trinity.tmp
668s * [Fri Nov  1 10:19:43 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa 2
669s * [Fri Nov  1 10:19:44 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta
669s Friday, November 1, 2024: 10:19:44	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta.gene_trans_map
669s 
669s 
669s #############################################################################
669s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_qual_and_norm.Trinity.fasta
669s #############################################################################
669s 
669s 
669s ./misc_run_tests/__test_runMe_with_jaccard_clip.sh
669s 
669s ##### Done Running Trinity #####
669s 
669s exit 0
669s #!/bin/bash -ve
669s 
669s ${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
669s 
669s 
669s      ______  ____   ____  ____   ____  ______  __ __
669s     |      ||    \ |    ||    \ |    ||      ||  |  |
669s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
669s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
669s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
669s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
669s       |__|  |__|\_||____||__|__||____|  |__|  |____/
669s 
669s     Trinity-v2.15.1
669s 
669s 
669s 
669s Left read files: $VAR1 = [
669s           'reads.left.fq.gz'
669s         ];
669s Right read files: $VAR1 = [
669s           'reads.right.fq.gz'
669s         ];
669s Friday, November 1, 2024: 10:19:44	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard
669s Friday, November 1, 2024: 10:19:44	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis
669s 
669s 
669s ----------------------------------------------------------------------------------
669s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
669s ----------------------------------------------------------------------------------
669s 
669s ---------------------------------------------------------------
669s ------------ In silico Read Normalization ---------------------
669s -- (Removing Excess Reads Beyond 200 Coverage --
669s ---------------------------------------------------------------
669s 
669s # running normalization on reads: $VAR1 = [
669s           [
669s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
669s           ],
669s           [
669s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
669s           ]
669s         ];
669s 
669s 
669s Friday, November 1, 2024: 10:19:44	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G  --max_cov 200 --min_cov 1 --CPU 1 --output /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together  --PARALLEL_STATS  
670s -prepping seqs
670s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
670s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
670s CMD finished (0 seconds)
670s CMD finished (0 seconds)
670s CMD: touch left.fa.ok
670s CMD finished (0 seconds)
670s CMD: touch right.fa.ok
670s CMD finished (0 seconds)
670s Done converting input files.CMD: cat left.fa right.fa > both.fa
670s CMD finished (0 seconds)
670s CMD: touch both.fa.ok
670s CMD finished (0 seconds)
670s -kmer counting.
670s -------------------------------------------
670s ----------- Jellyfish  --------------------
670s -- (building a k-mer catalog from reads) --
670s -------------------------------------------
670s 
670s CMD: jellyfish count -t 1 -m 25 -s 100000000  both.fa
672s CMD finished (2 seconds)
672s CMD: jellyfish histo -t 1 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
672s CMD finished (0 seconds)
672s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
672s CMD finished (0 seconds)
672s CMD: touch jellyfish.K25.min2.kmers.fa.success
672s CMD finished (0 seconds)
672s -generating stats files
672s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
672s -reading Kmer occurrences...
672s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
672s -reading Kmer occurrences...
672s 
672s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
672s 
672s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
673s STATS_GENERATION_TIME: 1 seconds.
673s CMD finished (1 seconds)
673s STATS_GENERATION_TIME: 1 seconds.
673s CMD finished (1 seconds)
673s CMD: touch left.fa.K25.stats.ok
673s CMD finished (0 seconds)
673s CMD: touch right.fa.K25.stats.ok
673s CMD finished (0 seconds)
673s -sorting each stats file by read name.
673s 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
673s 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
673s CMD finished (0 seconds)
673s CMD finished (0 seconds)
673s CMD: touch left.fa.K25.stats.sort.ok
673s CMD finished (0 seconds)
673s CMD: touch right.fa.K25.stats.sort.ok
673s CMD finished (0 seconds)
673s -defining normalized reads
673s 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
673s -opening left.fa.K25.stats.sort
673s -opening right.fa.K25.stats.sort
673s -done opening files.
673s CMD finished (0 seconds)
673s CMD: touch pairs.K25.stats.ok
673s CMD finished (0 seconds)
673s 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
674s 30472 / 30575 = 99.66% reads selected during normalization.
674s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
674s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
674s CMD finished (1 seconds)
674s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
674s CMD finished (0 seconds)
674s -search and capture.
674s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture.
674s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
674s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture.
674s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
674s CMD: touch /tmp/autopkgtest.xkSdGF/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
674s CMD finished (0 seconds)
674s CMD: touch /tmp/autopkgtest.xkSdGF/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
674s CMD finished (0 seconds)
674s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
674s CMD finished (0 seconds)
674s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
674s CMD finished (0 seconds)
674s -removing tmp dir /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/tmp_normalized_reads
674s 
674s 
674s Normalization complete. See outputs: 
674s 	/tmp/autopkgtest.xkSdGF/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
674s 	/tmp/autopkgtest.xkSdGF/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
674s Friday, November 1, 2024: 10:19:49	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/insilico_read_normalization/normalization.ok
674s Converting input files. (in parallel)Friday, November 1, 2024: 10:19:49	CMD: cat /tmp/autopkgtest.xkSdGF/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
674s Friday, November 1, 2024: 10:19:49	CMD: cat /tmp/autopkgtest.xkSdGF/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
674s Friday, November 1, 2024: 10:19:49	CMD: touch left.fa.ok
674s Friday, November 1, 2024: 10:19:49	CMD: touch right.fa.ok
674s Friday, November 1, 2024: 10:19:49	CMD: touch left.fa.ok right.fa.ok
674s Friday, November 1, 2024: 10:19:49	CMD: cat left.fa right.fa > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
674s Friday, November 1, 2024: 10:19:49	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa.ok
675s -------------------------------------------
675s ----------- Jellyfish  --------------------
675s -- (building a k-mer (25) catalog from reads) --
675s -------------------------------------------
675s 
675s * [Fri Nov  1 10:19:49 2024] Running CMD: jellyfish count -t 1 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
677s * [Fri Nov  1 10:19:52 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
677s * [Fri Nov  1 10:19:52 2024] Running CMD: jellyfish histo -t 1 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
677s ----------------------------------------------
677s --------------- Inchworm (K=25, asm) ---------------------
677s -- (Linear contig construction from k-mers) --
677s ----------------------------------------------
677s 
677s * [Fri Nov  1 10:19:52 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa.tmp
677s Kmer length set to: 25
677s Min assembly length set to: 25
677s Monitor turned on, set to: 1
677s min entropy set to: 1
677s setting number of threads to: 1
677s -setting parallel iworm mode.
677s -reading Kmer occurrences...
678s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
678s  done parsing 519541 Kmers, 519541 added, taking 1 seconds.
678s 
678s TIMING KMER_DB_BUILDING 1 s.
678s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
678s Pruned 4252 kmers from catalog.
678s 	Pruning time: 0 seconds = 0 minutes.
678s 
678s TIMING PRUNING 0 s.
678s -populating the kmer seed candidate list.
678s Kcounter hash size: 519541
678s Processed 515289 non-zero abundance kmers in kcounter.
678s -Not sorting list of kmers, given parallel mode in effect.
678s -beginning inchworm contig assembly.
678s Total kcounter hash size: 519541 vs. sorted list size: 515289
678s num threads set to: 1
678s Done opening file. tmp.iworm.fa.pid_34534.thread_0
679s 
679s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
679s 
679s TIMING CONTIG_BUILDING 1 s.
679s 
679s TIMING PROG_RUNTIME 2 s.
679s * [Fri Nov  1 10:19:54 2024] Running CMD: mv /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa.tmp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa
679s Friday, November 1, 2024: 10:19:54	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa.finished
679s --------------------------------------------------------
679s -------------------- Chrysalis -------------------------
679s -- (Contig Clustering & de Bruijn Graph Construction) --
679s --------------------------------------------------------
679s 
679s inchworm_target: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
679s bowtie_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
679s chrysalis_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa
679s * [Fri Nov  1 10:19:54 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/inchworm.fa 100 10 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100
679s * [Fri Nov  1 10:19:54 2024] Running CMD: /usr/bin/bowtie2-build --threads 1 -o 3 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 1>/dev/null
679s * [Fri Nov  1 10:19:54 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm.bowtie.nameSorted.bam" 
682s * [Fri Nov  1 10:19:57 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_scaffolds.txt
682s * [Fri Nov  1 10:19:57 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt
683s * [Fri Nov  1 10:19:58 2024] Running CMD: /usr/bin/sort --parallel=1 -T . -S 1G  -k9,9gr /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted
683s * [Fri Nov  1 10:19:58 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
683s * [Fri Nov  1 10:19:58 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/GraphFromIwormFasta.out
683s * [Fri Nov  1 10:19:58 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/bundled_iworm_contigs.fasta -min 200
683s * [Fri Nov  1 10:19:58 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa -f /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/readsToComponents.out -t 1 -max_mem_reads 50000000  -strand  -p 10 
687s * [Fri Nov  1 10:20:02 2024] Running CMD: /usr/bin/sort --parallel=1 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/readsToComponents.out > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/chrysalis/readsToComponents.out.sort
687s Friday, November 1, 2024: 10:20:02	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0
687s Friday, November 1, 2024: 10:20:02	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/partitioned_reads.files.list.ok
687s Friday, November 1, 2024: 10:20:02	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.xkSdGF/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
687s Friday, November 1, 2024: 10:20:02	CMD: touch recursive_trinity.cmds.ok
687s Friday, November 1, 2024: 10:20:02	CMD: touch recursive_trinity.cmds.ok
687s 
687s 
687s --------------------------------------------------------------------------------
687s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
687s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
687s --------------------------------------------------------------------------------
687s 
687s Friday, November 1, 2024: 10:20:02	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 1 -v -shuffle 
687s Number of Commands: 36
689s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
689s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
689s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
689s bt2 index files: $VAR1 = [];
689s Note - bowtie-build indices do not yet exist. Indexing genome now.
689s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
689s CMD: touch /tmp/autopkgtest.xkSdGF/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
689s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
689s 9900 reads; of these:
689s   9900 (100.00%) were unpaired; of these:
689s     5 (0.05%) aligned 0 times
689s     5821 (58.80%) aligned exactly 1 time
689s     4074 (41.15%) aligned >1 times
689s 99.95% overall alignment rate
689s CMD: touch /tmp/autopkgtest.xkSdGF/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
689s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
690s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
690s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
690s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
690s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
690s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
690s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
690s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
690s 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
690s 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 
690s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
690s 
690s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
690s 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
690s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
690s 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
690s 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 
690s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
690s -processing jaccard pair sensor
691s 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
691s 
[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
691s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
697s 
succeeded(1)   2.77778% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
697s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
697s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
697s bt2 index files: $VAR1 = [];
697s Note - bowtie-build indices do not yet exist. Indexing genome now.
697s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
698s CMD: touch /tmp/autopkgtest.xkSdGF/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
698s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
698s 6 reads; of these:
698s   6 (100.00%) were unpaired; of these:
698s     0 (0.00%) aligned 0 times
698s     6 (100.00%) aligned exactly 1 time
698s     0 (0.00%) aligned >1 times
698s 100.00% overall alignment rate
698s CMD: touch /tmp/autopkgtest.xkSdGF/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
698s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
698s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
698s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
698s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
698s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
698s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
698s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
698s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
698s 
698s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
698s 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
698s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
698s 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
698s 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 
698s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
698s -processing jaccard pair sensor
698s 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
698s 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
698s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
699s 
succeeded(2)   5.55556% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
699s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
699s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
699s bt2 index files: $VAR1 = [];
699s Note - bowtie-build indices do not yet exist. Indexing genome now.
699s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
699s CMD: touch /tmp/autopkgtest.xkSdGF/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
699s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
699s 29 reads; of these:
699s   29 (100.00%) were unpaired; of these:
699s     0 (0.00%) aligned 0 times
699s     29 (100.00%) aligned exactly 1 time
699s     0 (0.00%) aligned >1 times
699s 100.00% overall alignment rate
699s CMD: touch /tmp/autopkgtest.xkSdGF/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
699s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
699s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
699s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
699s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
699s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
699s 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
699s 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 
700s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
700s 
700s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
700s 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
700s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
700s 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
700s 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 
700s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
700s -processing jaccard pair sensor
700s 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
700s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
700s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
701s 
succeeded(3)   8.33333% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
701s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
701s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
701s bt2 index files: $VAR1 = [];
701s Note - bowtie-build indices do not yet exist. Indexing genome now.
701s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
701s CMD: touch /tmp/autopkgtest.xkSdGF/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
701s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
701s 33 reads; of these:
701s   33 (100.00%) were unpaired; of these:
701s     0 (0.00%) aligned 0 times
701s     33 (100.00%) aligned exactly 1 time
701s     0 (0.00%) aligned >1 times
701s 100.00% overall alignment rate
701s CMD: touch /tmp/autopkgtest.xkSdGF/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
701s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
701s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
701s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
701s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
701s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
701s 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
701s 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 
701s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
701s 
701s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
701s 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
701s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
701s 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
701s 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 
701s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
701s -processing jaccard pair sensor
701s 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
701s 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
701s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
703s 
succeeded(4)   11.1111% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
703s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
703s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
703s bt2 index files: $VAR1 = [];
703s Note - bowtie-build indices do not yet exist. Indexing genome now.
703s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
703s CMD: touch /tmp/autopkgtest.xkSdGF/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
703s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
703s 9 reads; of these:
703s   9 (100.00%) were unpaired; of these:
703s     0 (0.00%) aligned 0 times
703s     9 (100.00%) aligned exactly 1 time
703s     0 (0.00%) aligned >1 times
703s 100.00% overall alignment rate
703s CMD: touch /tmp/autopkgtest.xkSdGF/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
703s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
703s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
703s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
703s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
703s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
703s 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
703s 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 
703s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
703s 
703s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
703s 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
703s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
703s 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
703s 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 
703s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
703s -processing jaccard pair sensor
703s 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
703s 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
703s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
705s 
succeeded(5)   13.8889% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
705s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
705s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
705s bt2 index files: $VAR1 = [];
705s Note - bowtie-build indices do not yet exist. Indexing genome now.
705s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
705s CMD: touch /tmp/autopkgtest.xkSdGF/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
705s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
705s 8 reads; of these:
705s   8 (100.00%) were unpaired; of these:
705s     0 (0.00%) aligned 0 times
705s     8 (100.00%) aligned exactly 1 time
705s     0 (0.00%) aligned >1 times
705s 100.00% overall alignment rate
705s CMD: touch /tmp/autopkgtest.xkSdGF/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
705s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
705s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
705s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
705s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
705s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
705s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
705s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
705s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
705s 
705s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
705s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
705s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
705s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
705s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
705s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
705s -processing jaccard pair sensor
705s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
705s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
705s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
707s 
succeeded(6)   16.6667% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
707s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
707s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
707s bt2 index files: $VAR1 = [];
707s Note - bowtie-build indices do not yet exist. Indexing genome now.
707s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
707s CMD: touch /tmp/autopkgtest.xkSdGF/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
707s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
708s 4987 reads; of these:
708s   4987 (100.00%) were unpaired; of these:
708s     2 (0.04%) aligned 0 times
708s     2643 (53.00%) aligned exactly 1 time
708s     2342 (46.96%) aligned >1 times
708s 99.96% overall alignment rate
708s CMD: touch /tmp/autopkgtest.xkSdGF/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
708s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
708s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
708s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
708s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
708s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
708s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
708s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
708s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
708s 
708s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
708s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
708s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
708s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
708s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
708s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
708s -processing jaccard pair sensor
708s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
708s 
[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
708s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
712s 
succeeded(7)   19.4444% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
712s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
712s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
712s bt2 index files: $VAR1 = [];
712s Note - bowtie-build indices do not yet exist. Indexing genome now.
712s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
712s CMD: touch /tmp/autopkgtest.xkSdGF/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
712s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
712s 15 reads; of these:
712s   15 (100.00%) were unpaired; of these:
712s     0 (0.00%) aligned 0 times
712s     15 (100.00%) aligned exactly 1 time
712s     0 (0.00%) aligned >1 times
712s 100.00% overall alignment rate
712s CMD: touch /tmp/autopkgtest.xkSdGF/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
712s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
712s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
712s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
712s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
712s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
712s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
712s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
712s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
712s 
712s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
712s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
712s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
712s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
712s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
712s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
712s -processing jaccard pair sensor
712s 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
712s 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
712s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
714s 
succeeded(8)   22.2222% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
714s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
714s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
714s bt2 index files: $VAR1 = [];
714s Note - bowtie-build indices do not yet exist. Indexing genome now.
714s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
714s CMD: touch /tmp/autopkgtest.xkSdGF/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
714s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
714s 17 reads; of these:
714s   17 (100.00%) were unpaired; of these:
714s     0 (0.00%) aligned 0 times
714s     17 (100.00%) aligned exactly 1 time
714s     0 (0.00%) aligned >1 times
714s 100.00% overall alignment rate
714s CMD: touch /tmp/autopkgtest.xkSdGF/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
714s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
714s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
714s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
714s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
714s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
714s 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
714s 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 
714s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
714s 
714s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
714s 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
714s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
714s 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
714s 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 
714s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
714s -processing jaccard pair sensor
714s 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
714s 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
714s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
716s 
succeeded(9)   25% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
716s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
716s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
716s bt2 index files: $VAR1 = [];
716s Note - bowtie-build indices do not yet exist. Indexing genome now.
716s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
717s CMD: touch /tmp/autopkgtest.xkSdGF/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
717s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
717s 7052 reads; of these:
717s   7052 (100.00%) were unpaired; of these:
717s     4 (0.06%) aligned 0 times
717s     5120 (72.60%) aligned exactly 1 time
717s     1928 (27.34%) aligned >1 times
717s 99.94% overall alignment rate
717s CMD: touch /tmp/autopkgtest.xkSdGF/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
717s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
717s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
717s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
717s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
717s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
717s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
717s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
717s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
717s 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
717s 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 
717s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
717s 
718s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
718s 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
718s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
718s 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
718s 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 
718s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
718s -processing jaccard pair sensor
718s 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
718s 
[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
718s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
728s 
succeeded(10)   27.7778% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
728s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
728s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
728s bt2 index files: $VAR1 = [];
728s Note - bowtie-build indices do not yet exist. Indexing genome now.
728s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
728s CMD: touch /tmp/autopkgtest.xkSdGF/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
728s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
728s 7 reads; of these:
728s   7 (100.00%) were unpaired; of these:
728s     3 (42.86%) aligned 0 times
728s     4 (57.14%) aligned exactly 1 time
728s     0 (0.00%) aligned >1 times
728s 57.14% overall alignment rate
728s CMD: touch /tmp/autopkgtest.xkSdGF/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
728s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
728s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
728s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
728s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
728s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
728s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
728s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
728s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
728s 
728s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
728s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
728s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
728s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
728s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
728s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
728s -processing jaccard pair sensor
728s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
728s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
728s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
729s 
succeeded(11)   30.5556% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
729s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
729s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
729s bt2 index files: $VAR1 = [];
729s Note - bowtie-build indices do not yet exist. Indexing genome now.
729s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
730s CMD: touch /tmp/autopkgtest.xkSdGF/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
730s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
730s 28 reads; of these:
730s   28 (100.00%) were unpaired; of these:
730s     0 (0.00%) aligned 0 times
730s     28 (100.00%) aligned exactly 1 time
730s     0 (0.00%) aligned >1 times
730s 100.00% overall alignment rate
730s CMD: touch /tmp/autopkgtest.xkSdGF/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
730s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
730s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
730s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
730s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
730s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
730s 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
730s 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 
730s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
730s 
730s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
730s 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
730s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
730s 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
730s 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 
730s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
730s -processing jaccard pair sensor
730s 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
730s 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
730s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c22.trinity.reads.fa.out/inchworm.fa.clipped.fa
731s 
succeeded(12)   33.3333% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
731s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
731s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
731s bt2 index files: $VAR1 = [];
731s Note - bowtie-build indices do not yet exist. Indexing genome now.
731s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
732s CMD: touch /tmp/autopkgtest.xkSdGF/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
732s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
732s 24 reads; of these:
732s   24 (100.00%) were unpaired; of these:
732s     0 (0.00%) aligned 0 times
732s     24 (100.00%) aligned exactly 1 time
732s     0 (0.00%) aligned >1 times
732s 100.00% overall alignment rate
732s CMD: touch /tmp/autopkgtest.xkSdGF/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
732s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
732s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
732s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
732s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
732s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
732s 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
732s 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 
732s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
732s 
732s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
732s 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
732s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
732s 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
732s 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 
732s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
732s -processing jaccard pair sensor
732s 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
732s 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
732s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c19.trinity.reads.fa.out/inchworm.fa.clipped.fa
734s 
succeeded(13)   36.1111% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
734s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2 --SS_lib_type F 
734s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
734s bt2 index files: $VAR1 = [];
734s Note - bowtie-build indices do not yet exist. Indexing genome now.
734s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa
734s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/iworm.fa._bt2_idx_.ok
734s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam" 
735s 5130 reads; of these:
735s   5130 (100.00%) were unpaired; of these:
735s     6 (0.12%) aligned 0 times
735s     4306 (83.94%) aligned exactly 1 time
735s     818 (15.95%) aligned >1 times
735s 99.88% overall alignment rate
735s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.ok
735s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam F
735s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
735s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam
735s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
735s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.bam
735s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.sam
735s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.-.sam
735s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie2.coordSorted.bam.+.bam bowtie_alignments.for_jaccard.bam
735s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
735s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
735s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
735s 
735s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
735s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
735s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/read_partitions/Fb_0/CBin_0/c2.trinity.reads.fa.out/jaccard_clip_workdir/bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
735s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
735s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
735s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
735s -processing jaccard pair sensor
736s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
736s 
[1000 lines read]  scaff:a25;2 lend:1  rend:45     
[2000 lines read]  scaff:a3;25 lend:514  rend:589     
[3000 lines read]  scaff:a3;25 lend:4028  rend:4299     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
736s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
740s 
succeeded(14)   38.8889% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
740s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
740s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
740s bt2 index files: $VAR1 = [];
740s Note - bowtie-build indices do not yet exist. Indexing genome now.
740s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
740s CMD: touch /tmp/autopkgtest.xkSdGF/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
740s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
741s 3374 reads; of these:
741s   3374 (100.00%) were unpaired; of these:
741s     1 (0.03%) aligned 0 times
741s     2870 (85.06%) aligned exactly 1 time
741s     503 (14.91%) aligned >1 times
741s 99.97% overall alignment rate
741s CMD: touch /tmp/autopkgtest.xkSdGF/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
741s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
741s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
741s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
741s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
741s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
741s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
741s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
741s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
741s 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
741s 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 
741s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
741s 
741s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
741s 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
741s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
741s 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
741s 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 
741s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
741s -processing jaccard pair sensor
741s 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
741s 
[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
741s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
744s 
succeeded(15)   41.6667% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
744s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
744s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
744s bt2 index files: $VAR1 = [];
744s Note - bowtie-build indices do not yet exist. Indexing genome now.
744s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
745s CMD: touch /tmp/autopkgtest.xkSdGF/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
745s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
745s 6 reads; of these:
745s   6 (100.00%) were unpaired; of these:
745s     0 (0.00%) aligned 0 times
745s     6 (100.00%) aligned exactly 1 time
745s     0 (0.00%) aligned >1 times
745s 100.00% overall alignment rate
745s CMD: touch /tmp/autopkgtest.xkSdGF/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
745s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
745s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
745s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
745s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
745s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
745s 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
745s 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 
745s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
745s 
745s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
745s 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
745s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
745s 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
745s 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 
745s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
745s -processing jaccard pair sensor
745s 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
745s 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
745s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
746s 
succeeded(16)   44.4444% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
746s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
746s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
746s bt2 index files: $VAR1 = [];
746s Note - bowtie-build indices do not yet exist. Indexing genome now.
746s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
746s CMD: touch /tmp/autopkgtest.xkSdGF/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
746s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
746s 8 reads; of these:
746s   8 (100.00%) were unpaired; of these:
746s     0 (0.00%) aligned 0 times
746s     8 (100.00%) aligned exactly 1 time
746s     0 (0.00%) aligned >1 times
746s 100.00% overall alignment rate
746s CMD: touch /tmp/autopkgtest.xkSdGF/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
746s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
746s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
746s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
746s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
746s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
746s 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
746s 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 
746s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
746s 
746s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
746s 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
746s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
746s 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
746s 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 
746s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
746s -processing jaccard pair sensor
746s 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
746s 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
746s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
748s 
succeeded(17)   47.2222% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
748s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
748s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
748s bt2 index files: $VAR1 = [];
748s Note - bowtie-build indices do not yet exist. Indexing genome now.
748s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
748s CMD: touch /tmp/autopkgtest.xkSdGF/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
748s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
748s 14 reads; of these:
748s   14 (100.00%) were unpaired; of these:
748s     0 (0.00%) aligned 0 times
748s     14 (100.00%) aligned exactly 1 time
748s     0 (0.00%) aligned >1 times
748s 100.00% overall alignment rate
748s CMD: touch /tmp/autopkgtest.xkSdGF/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
748s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
748s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
748s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
748s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
748s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
748s 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
748s 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 
748s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
748s 
748s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
748s 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
748s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
748s 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
748s 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 
748s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
748s -processing jaccard pair sensor
748s 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
748s 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
748s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
750s 
succeeded(18)   50% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
750s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
750s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
750s bt2 index files: $VAR1 = [];
750s Note - bowtie-build indices do not yet exist. Indexing genome now.
750s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
750s CMD: touch /tmp/autopkgtest.xkSdGF/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
750s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
750s 15 reads; of these:
750s   15 (100.00%) were unpaired; of these:
750s     0 (0.00%) aligned 0 times
750s     15 (100.00%) aligned exactly 1 time
750s     0 (0.00%) aligned >1 times
750s 100.00% overall alignment rate
750s CMD: touch /tmp/autopkgtest.xkSdGF/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
750s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
750s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
750s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
750s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
750s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
750s 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
750s 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 
750s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
750s 
750s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
750s 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
750s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
750s 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
750s 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 
750s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
750s -processing jaccard pair sensor
750s 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
750s 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
750s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
752s 
succeeded(19)   52.7778% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
752s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
752s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
752s bt2 index files: $VAR1 = [];
752s Note - bowtie-build indices do not yet exist. Indexing genome now.
752s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
752s CMD: touch /tmp/autopkgtest.xkSdGF/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
752s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
752s 2351 reads; of these:
752s   2351 (100.00%) were unpaired; of these:
752s     1 (0.04%) aligned 0 times
752s     1736 (73.84%) aligned exactly 1 time
752s     614 (26.12%) aligned >1 times
752s 99.96% overall alignment rate
752s CMD: touch /tmp/autopkgtest.xkSdGF/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
752s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
752s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
752s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
752s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
752s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
752s 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
752s 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 
752s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
752s 
752s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
752s 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
752s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
752s 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
752s 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 
752s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
752s -processing jaccard pair sensor
753s 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
753s 
[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
753s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
757s 
succeeded(20)   55.5556% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
757s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
757s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
757s bt2 index files: $VAR1 = [];
757s Note - bowtie-build indices do not yet exist. Indexing genome now.
757s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
757s CMD: touch /tmp/autopkgtest.xkSdGF/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
757s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
757s 1875 reads; of these:
757s   1875 (100.00%) were unpaired; of these:
757s     2 (0.11%) aligned 0 times
757s     1543 (82.29%) aligned exactly 1 time
757s     330 (17.60%) aligned >1 times
757s 99.89% overall alignment rate
757s CMD: touch /tmp/autopkgtest.xkSdGF/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
757s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
757s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
757s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
757s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
757s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
757s 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
757s 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 
757s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
757s 
757s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
757s 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
757s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
757s 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
757s 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 
757s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
757s -processing jaccard pair sensor
757s 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
757s 
[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
757s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
760s 
succeeded(21)   58.3333% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
760s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
760s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
760s bt2 index files: $VAR1 = [];
760s Note - bowtie-build indices do not yet exist. Indexing genome now.
760s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
761s CMD: touch /tmp/autopkgtest.xkSdGF/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
761s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
761s 40 reads; of these:
761s   40 (100.00%) were unpaired; of these:
761s     0 (0.00%) aligned 0 times
761s     36 (90.00%) aligned exactly 1 time
761s     4 (10.00%) aligned >1 times
761s 100.00% overall alignment rate
761s CMD: touch /tmp/autopkgtest.xkSdGF/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
761s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
761s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
761s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
761s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
761s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
761s 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
761s 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 
761s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
761s 
761s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
761s 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
761s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
761s 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
761s 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 
761s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
761s -processing jaccard pair sensor
761s 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
761s 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
761s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
763s 
succeeded(22)   61.1111% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
763s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
763s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
763s bt2 index files: $VAR1 = [];
763s Note - bowtie-build indices do not yet exist. Indexing genome now.
763s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
763s CMD: touch /tmp/autopkgtest.xkSdGF/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
763s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
763s 28 reads; of these:
763s   28 (100.00%) were unpaired; of these:
763s     0 (0.00%) aligned 0 times
763s     28 (100.00%) aligned exactly 1 time
763s     0 (0.00%) aligned >1 times
763s 100.00% overall alignment rate
763s CMD: touch /tmp/autopkgtest.xkSdGF/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
763s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
763s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
763s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
763s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
763s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
763s 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
763s 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 
763s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
763s 
763s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
763s 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
763s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
763s 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
763s 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 
763s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
763s -processing jaccard pair sensor
763s 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
763s 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
763s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
765s 
succeeded(23)   63.8889% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
765s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
765s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
765s bt2 index files: $VAR1 = [];
765s Note - bowtie-build indices do not yet exist. Indexing genome now.
765s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
765s CMD: touch /tmp/autopkgtest.xkSdGF/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
765s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
765s 29 reads; of these:
765s   29 (100.00%) were unpaired; of these:
765s     0 (0.00%) aligned 0 times
765s     23 (79.31%) aligned exactly 1 time
765s     6 (20.69%) aligned >1 times
765s 100.00% overall alignment rate
765s CMD: touch /tmp/autopkgtest.xkSdGF/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
765s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
765s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
765s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
765s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
765s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
765s 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
765s 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 
765s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
765s 
765s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
765s 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
765s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
765s 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
765s 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 
765s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
765s -processing jaccard pair sensor
765s 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
765s 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
765s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
767s 
succeeded(24)   66.6667% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
767s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
767s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
767s bt2 index files: $VAR1 = [];
767s Note - bowtie-build indices do not yet exist. Indexing genome now.
767s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
767s CMD: touch /tmp/autopkgtest.xkSdGF/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
767s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
767s 8 reads; of these:
767s   8 (100.00%) were unpaired; of these:
767s     0 (0.00%) aligned 0 times
767s     8 (100.00%) aligned exactly 1 time
767s     0 (0.00%) aligned >1 times
767s 100.00% overall alignment rate
767s CMD: touch /tmp/autopkgtest.xkSdGF/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
767s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
767s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
767s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
767s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
767s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
767s 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
767s 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 
767s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
767s 
767s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
767s 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
767s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
767s 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
767s 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 
767s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
767s -processing jaccard pair sensor
767s 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
767s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
767s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
768s 
succeeded(25)   69.4444% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
768s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
768s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
768s bt2 index files: $VAR1 = [];
768s Note - bowtie-build indices do not yet exist. Indexing genome now.
768s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
768s CMD: touch /tmp/autopkgtest.xkSdGF/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
768s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
768s 81 reads; of these:
768s   81 (100.00%) were unpaired; of these:
768s     0 (0.00%) aligned 0 times
768s     78 (96.30%) aligned exactly 1 time
768s     3 (3.70%) aligned >1 times
768s 100.00% overall alignment rate
768s CMD: touch /tmp/autopkgtest.xkSdGF/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
768s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
768s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
768s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
768s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
768s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
768s 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
768s 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 
769s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
769s 
769s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
769s 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
769s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
769s 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
769s 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 
769s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
769s -processing jaccard pair sensor
769s 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
769s 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
769s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
770s 
succeeded(26)   72.2222% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
770s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
770s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
770s bt2 index files: $VAR1 = [];
770s Note - bowtie-build indices do not yet exist. Indexing genome now.
770s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
771s CMD: touch /tmp/autopkgtest.xkSdGF/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
771s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
771s 13 reads; of these:
771s   13 (100.00%) were unpaired; of these:
771s     0 (0.00%) aligned 0 times
771s     13 (100.00%) aligned exactly 1 time
771s     0 (0.00%) aligned >1 times
771s 100.00% overall alignment rate
771s CMD: touch /tmp/autopkgtest.xkSdGF/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
771s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
771s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
771s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
771s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
771s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
771s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
771s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
771s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
771s 
771s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
771s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
771s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
771s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
771s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
771s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
771s -processing jaccard pair sensor
771s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
771s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
771s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
772s 
succeeded(27)   75% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
772s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
772s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
772s bt2 index files: $VAR1 = [];
772s Note - bowtie-build indices do not yet exist. Indexing genome now.
772s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
772s CMD: touch /tmp/autopkgtest.xkSdGF/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
772s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
773s 1556 reads; of these:
773s   1556 (100.00%) were unpaired; of these:
773s     1 (0.06%) aligned 0 times
773s     1328 (85.35%) aligned exactly 1 time
773s     227 (14.59%) aligned >1 times
773s 99.94% overall alignment rate
773s CMD: touch /tmp/autopkgtest.xkSdGF/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
773s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
773s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
773s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
773s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
773s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
773s 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
773s 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 
773s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
773s 
773s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
773s 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
773s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
773s 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
773s 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 
773s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
773s -processing jaccard pair sensor
773s 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
773s 
[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
773s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
776s 
succeeded(28)   77.7778% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
776s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
776s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
776s bt2 index files: $VAR1 = [];
776s Note - bowtie-build indices do not yet exist. Indexing genome now.
776s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
776s CMD: touch /tmp/autopkgtest.xkSdGF/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
776s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
776s 20 reads; of these:
776s   20 (100.00%) were unpaired; of these:
776s     0 (0.00%) aligned 0 times
776s     20 (100.00%) aligned exactly 1 time
776s     0 (0.00%) aligned >1 times
776s 100.00% overall alignment rate
776s CMD: touch /tmp/autopkgtest.xkSdGF/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
776s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
776s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
776s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
776s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
776s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
776s 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
776s 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 
776s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
776s 
776s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
776s 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
776s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
776s 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
776s 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 
776s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
776s -processing jaccard pair sensor
776s 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
776s 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
776s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
779s 
succeeded(29)   80.5556% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
779s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
779s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
779s bt2 index files: $VAR1 = [];
779s Note - bowtie-build indices do not yet exist. Indexing genome now.
779s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
779s CMD: touch /tmp/autopkgtest.xkSdGF/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
779s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
779s 8656 reads; of these:
779s   8656 (100.00%) were unpaired; of these:
779s     6 (0.07%) aligned 0 times
779s     5677 (65.58%) aligned exactly 1 time
779s     2973 (34.35%) aligned >1 times
779s 99.93% overall alignment rate
779s CMD: touch /tmp/autopkgtest.xkSdGF/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
779s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
780s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
780s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
780s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
780s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
780s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
780s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
780s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
780s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
780s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
780s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
780s 
780s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
780s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
780s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
780s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
780s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
780s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
780s -processing jaccard pair sensor
781s 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
781s 
[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
781s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
786s 
succeeded(30)   83.3333% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
786s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
786s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
786s bt2 index files: $VAR1 = [];
786s Note - bowtie-build indices do not yet exist. Indexing genome now.
786s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
786s CMD: touch /tmp/autopkgtest.xkSdGF/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
786s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
787s 9 reads; of these:
787s   9 (100.00%) were unpaired; of these:
787s     0 (0.00%) aligned 0 times
787s     9 (100.00%) aligned exactly 1 time
787s     0 (0.00%) aligned >1 times
787s 100.00% overall alignment rate
787s CMD: touch /tmp/autopkgtest.xkSdGF/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
787s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
787s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
787s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
787s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
787s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
787s 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
787s 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 
787s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
787s 
787s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
787s 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
787s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
787s 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
787s 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 
787s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
787s -processing jaccard pair sensor
787s 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
787s 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
787s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
788s 
succeeded(31)   86.1111% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
788s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
788s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
788s bt2 index files: $VAR1 = [];
788s Note - bowtie-build indices do not yet exist. Indexing genome now.
788s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
788s CMD: touch /tmp/autopkgtest.xkSdGF/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
788s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
789s 20 reads; of these:
789s   20 (100.00%) were unpaired; of these:
789s     0 (0.00%) aligned 0 times
789s     20 (100.00%) aligned exactly 1 time
789s     0 (0.00%) aligned >1 times
789s 100.00% overall alignment rate
789s CMD: touch /tmp/autopkgtest.xkSdGF/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
789s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
789s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
789s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
789s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
789s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
789s 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
789s 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 
789s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
789s 
789s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
789s 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
789s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
789s 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
789s 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 
789s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
789s -processing jaccard pair sensor
789s 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
789s 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
789s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
790s 
succeeded(32)   88.8889% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
790s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
790s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
790s bt2 index files: $VAR1 = [];
790s Note - bowtie-build indices do not yet exist. Indexing genome now.
790s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
790s CMD: touch /tmp/autopkgtest.xkSdGF/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
790s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
790s 11 reads; of these:
790s   11 (100.00%) were unpaired; of these:
790s     0 (0.00%) aligned 0 times
790s     11 (100.00%) aligned exactly 1 time
790s     0 (0.00%) aligned >1 times
790s 100.00% overall alignment rate
791s CMD: touch /tmp/autopkgtest.xkSdGF/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
791s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
791s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
791s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
791s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
791s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
791s 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
791s 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 
791s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
791s 
791s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
791s 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
791s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
791s 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
791s 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 
791s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
791s -processing jaccard pair sensor
791s 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
791s 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
791s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
792s 
succeeded(33)   91.6667% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
792s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
792s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
792s bt2 index files: $VAR1 = [];
792s Note - bowtie-build indices do not yet exist. Indexing genome now.
792s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
792s CMD: touch /tmp/autopkgtest.xkSdGF/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
792s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
792s 9 reads; of these:
792s   9 (100.00%) were unpaired; of these:
792s     0 (0.00%) aligned 0 times
792s     9 (100.00%) aligned exactly 1 time
792s     0 (0.00%) aligned >1 times
792s 100.00% overall alignment rate
792s CMD: touch /tmp/autopkgtest.xkSdGF/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
792s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
792s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
792s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
792s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
792s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
792s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl --sam bowtie_alignments.for_jaccard.bam -W 100 > bowtie_alignments.for_jaccard.bam.J100.wig
792s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl --sam bowtie_alignments.for_jaccard.bam --max_insert_size 500 --min_insert_size 100 
792s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
792s 
792s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
792s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n bowtie_alignments.for_jaccard.bam.read_coords > bowtie_alignments.for_jaccard.bam.read_coords.sort_by_readname
792s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
792s CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.coord_sorted
792s CMD: /usr/lib/trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags bowtie_alignments.for_jaccard.bam.frag_coords -W 100  --pseudocounts 1 
792s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
792s -processing jaccard pair sensor
792s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.wig
792s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
792s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
795s 
succeeded(34)   94.4444% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
795s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
795s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
795s bt2 index files: $VAR1 = [];
795s Note - bowtie-build indices do not yet exist. Indexing genome now.
795s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
795s CMD: touch /tmp/autopkgtest.xkSdGF/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
795s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
796s 11272 reads; of these:
796s   11272 (100.00%) were unpaired; of these:
796s     2 (0.02%) aligned 0 times
796s     1241 (11.01%) aligned exactly 1 time
796s     10029 (88.97%) aligned >1 times
796s 99.98% overall alignment rate
796s CMD: touch /tmp/autopkgtest.xkSdGF/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
796s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
797s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
798s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
798s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
798s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
798s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
798s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
798s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
798s 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
798s 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 
798s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
798s 
799s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
799s 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
799s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
799s 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
799s 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 
799s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
799s -processing jaccard pair sensor
800s 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
801s 
[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
801s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
807s 
succeeded(35)   97.2222% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
807s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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 
807s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/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
807s bt2 index files: $VAR1 = [];
807s Note - bowtie-build indices do not yet exist. Indexing genome now.
807s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
807s CMD: touch /tmp/autopkgtest.xkSdGF/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
807s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 2 --no-unal -f -x /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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" 
807s 18 reads; of these:
807s   18 (100.00%) were unpaired; of these:
807s     0 (0.00%) aligned 0 times
807s     18 (100.00%) aligned exactly 1 time
807s     0 (0.00%) aligned >1 times
807s 100.00% overall alignment rate
807s CMD: touch /tmp/autopkgtest.xkSdGF/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
807s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/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
807s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/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
807s CMD: samtools index /tmp/autopkgtest.xkSdGF/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
807s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/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
807s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
807s 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
807s 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 
807s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
807s 
807s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
807s 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
807s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
807s 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
807s 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 
807s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
807s -processing jaccard pair sensor
807s 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
807s 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
807s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
808s 
succeeded(36)   100% completed.    
808s 
808s All commands completed successfully. :-)
808s 
808s 
808s 
808s ** Harvesting all assembled transcripts into a single multi-fasta file...
808s 
808s Friday, November 1, 2024: 10:22:03	CMD: find /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/Trinity.tmp
808s * [Fri Nov  1 10:22:03 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa 1
809s * [Fri Nov  1 10:22:04 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta
809s Friday, November 1, 2024: 10:22:04	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta.gene_trans_map
809s 
809s 
809s #############################################################################
809s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/__test_trinity_w_jaccard.Trinity.fasta
809s #############################################################################
809s 
809s 
809s ./misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh
809s 
809s 
809s exit 0
809s #!/bin/bash -ve
809s 
809s 
809s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
809s     gunzip -c reads.right.fq.gz > reads.right.fq
809s fi
809s 
809s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
809s     gunzip -c reads.left.fq.gz > reads.left.fq
809s fi
809s 
809s if [ -e reads2.right.fq.gz ] && [ ! -e reads2.right.fq ]; then
809s     gunzip -c reads2.right.fq.gz > reads2.right.fq
809s fi
809s 
809s if [ -e reads2.left.fq.gz ] && [ ! -e reads2.left.fq ]; then
809s     gunzip -c reads2.left.fq.gz > reads2.left.fq
809s fi
809s 
809s 
809s #######################################################
809s ##  Run Trinity to Generate Transcriptome Assemblies ##
809s #######################################################
809s 
809s CPU=$(nproc || sysctl -n hw.physicalcpu)
809s 
809s ${TRINITY_HOME}/Trinity --seqType fq \
809s               --max_memory 2G \
809s               --left reads.left.fq,reads2.left.fq \
809s               --right reads.right.fq,reads2.right.fq \
809s               --SS_lib_type RF \
809s               --CPU ${CPU} \
809s               --trimmomatic \
809s               --normalize_reads \
809s               --normalize_by_read_set \
809s               --output trinity_trim_and_norm_outdir
809s 
809s 
809s      ______  ____   ____  ____   ____  ______  __ __
809s     |      ||    \ |    ||    \ |    ||      ||  |  |
809s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
809s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
809s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
809s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
809s       |__|  |__|\_||____||__|__||____|  |__|  |____/
809s 
809s     Trinity-v2.15.1
809s 
809s 
809s 
809s Left read files: $VAR1 = [
809s           'reads.left.fq',
809s           'reads2.left.fq'
809s         ];
809s Right read files: $VAR1 = [
809s           'reads.right.fq',
809s           'reads2.right.fq'
809s         ];
809s Friday, November 1, 2024: 10:22:04	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir
809s Friday, November 1, 2024: 10:22:04	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis
809s 
809s 
809s ----------------------------------------------------------------------------------
809s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
809s ----------------------------------------------------------------------------------
809s 
809s ---------------------------------------------------------------
809s ------ Quality Trimming Via Trimmomatic  ---------------------
809s << ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >>
809s ---------------------------------------------------------------
809s 
809s 
809s ## Running Trimmomatic on read files: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq, /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq
809s Friday, November 1, 2024: 10:22:04	CMD: java  -jar /usr/share/java/trimmomatic.jar PE -threads 2  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.xkSdGF/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 
809s TrimmomaticPE: Started with arguments:
809s  -threads 2 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq /tmp/autopkgtest.xkSdGF/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
809s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
809s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
810s Quality encoding detected as phred33
810s 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%)
810s TrimmomaticPE: Completed successfully
810s Friday, November 1, 2024: 10:22:05	CMD: cp reads.left.fq.P.qtrim reads.left.fq.PwU.qtrim.fq
810s Friday, November 1, 2024: 10:22:05	CMD: cp reads.right.fq.P.qtrim reads.right.fq.PwU.qtrim.fq
810s Friday, November 1, 2024: 10:22:05	CMD: touch trimmomatic.ok
810s Friday, November 1, 2024: 10:22:05	CMD: gzip reads.left.fq.P.qtrim reads.left.fq.U.qtrim reads.right.fq.P.qtrim reads.right.fq.U.qtrim &
810s 
810s ## Running Trimmomatic on read files: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq, /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq
810s Friday, November 1, 2024: 10:22:05	CMD: java  -jar /usr/share/java/trimmomatic.jar PE -threads 2  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq /tmp/autopkgtest.xkSdGF/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 
810s TrimmomaticPE: Started with arguments:
810s  -threads 2 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq /tmp/autopkgtest.xkSdGF/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
810s Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
810s ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
810s Quality encoding detected as phred33
811s 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%)
811s TrimmomaticPE: Completed successfully
811s Friday, November 1, 2024: 10:22:06	CMD: cp reads2.left.fq.P.qtrim reads2.left.fq.PwU.qtrim.fq
811s Friday, November 1, 2024: 10:22:06	CMD: cp reads2.right.fq.P.qtrim reads2.right.fq.PwU.qtrim.fq
811s Friday, November 1, 2024: 10:22:06	CMD: touch trimmomatic.ok
811s Friday, November 1, 2024: 10:22:06	CMD: gzip reads2.left.fq.P.qtrim reads2.left.fq.U.qtrim reads2.right.fq.P.qtrim reads2.right.fq.U.qtrim &
811s ---------------------------------------------------------------
811s ------------ In silico Read Normalization ---------------------
811s -- (Removing Excess Reads Beyond 200 Coverage --
811s ---------------------------------------------------------------
811s 
811s 
811s ## Running in silico normalization, processing each read set separately
811s # running normalization on reads: $VAR1 = [
811s           [
811s             'reads.left.fq.PwU.qtrim.fq'
811s           ],
811s           [
811s             'reads.right.fq.PwU.qtrim.fq'
811s           ]
811s         ];
811s 
811s 
811s Friday, November 1, 2024: 10:22:06	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.xkSdGF/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  
811s -prepping seqs
811s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.left.fq.PwU.qtrim.fq >> left.fa
811s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.right.fq.PwU.qtrim.fq >> right.fa
811s CMD finished (0 seconds)
811s CMD finished (0 seconds)
811s CMD: touch left.fa.ok
811s CMD finished (0 seconds)
811s CMD: touch right.fa.ok
811s CMD finished (0 seconds)
811s Done converting input files.CMD: cat left.fa right.fa > both.fa
811s CMD finished (0 seconds)
811s CMD: touch both.fa.ok
811s CMD finished (0 seconds)
811s -kmer counting.
811s -------------------------------------------
811s ----------- Jellyfish  --------------------
811s -- (building a k-mer catalog from reads) --
811s -------------------------------------------
811s 
811s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
813s CMD finished (2 seconds)
813s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
813s CMD finished (0 seconds)
813s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
813s CMD finished (0 seconds)
813s CMD: touch jellyfish.K25.min2.kmers.fa.success
813s CMD finished (0 seconds)
813s -generating stats files
813s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
813s -reading Kmer occurrences...
813s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
813s -reading Kmer occurrences...
813s 
813s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
813s 
813s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
813s STATS_GENERATION_TIME: 0 seconds.
813s CMD finished (0 seconds)
813s STATS_GENERATION_TIME: 0 seconds.
814s CMD finished (0 seconds)
814s CMD: touch left.fa.K25.stats.ok
814s CMD finished (0 seconds)
814s CMD: touch right.fa.K25.stats.ok
814s CMD finished (0 seconds)
814s -sorting each stats file by read name.
814s 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
814s 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
814s CMD finished (1 seconds)
814s CMD finished (0 seconds)
814s CMD: touch left.fa.K25.stats.sort.ok
814s CMD finished (0 seconds)
814s CMD: touch right.fa.K25.stats.sort.ok
814s CMD finished (0 seconds)
814s -defining normalized reads
814s 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
814s -opening left.fa.K25.stats.sort
814s -opening right.fa.K25.stats.sort
814s -done opening files.
814s CMD finished (0 seconds)
814s CMD: touch pairs.K25.stats.ok
814s CMD finished (0 seconds)
814s 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
814s 27678 / 27726 = 99.83% reads selected during normalization.
814s 0 / 27726 = 0.00% reads discarded as likely aberrant based on coverage profiles.
814s 0 / 27726 = 0.00% reads discarded as below minimum coverage threshold=1
814s CMD finished (0 seconds)
814s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
814s CMD finished (0 seconds)
814s -search and capture.
815s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/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.
815s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.left.fq.PwU.qtrim.fq
815s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/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.
815s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads.right.fq.PwU.qtrim.fq
815s CMD: touch /tmp/autopkgtest.xkSdGF/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
815s CMD finished (0 seconds)
815s CMD: touch /tmp/autopkgtest.xkSdGF/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
815s CMD finished (0 seconds)
815s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
815s CMD finished (0 seconds)
815s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
815s CMD finished (0 seconds)
815s -removing tmp dir /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/tmp_normalized_reads
815s 
815s 
815s Normalization complete. See outputs: 
815s 	/tmp/autopkgtest.xkSdGF/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
815s 	/tmp/autopkgtest.xkSdGF/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
815s Friday, November 1, 2024: 10:22:10	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/normalization.ok
815s # running normalization on reads: $VAR1 = [
815s           [
815s             'reads2.left.fq.PwU.qtrim.fq'
815s           ],
815s           [
815s             'reads2.right.fq.PwU.qtrim.fq'
815s           ]
815s         ];
815s 
815s 
815s Friday, November 1, 2024: 10:22:10	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.xkSdGF/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  
815s -prepping seqs
815s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.left.fq.PwU.qtrim.fq >> left.fa
815s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.right.fq.PwU.qtrim.fq >> right.fa
815s CMD finished (0 seconds)
815s CMD finished (0 seconds)
815s CMD: touch left.fa.ok
815s CMD finished (0 seconds)
815s CMD: touch right.fa.ok
815s CMD finished (0 seconds)
815s Done converting input files.CMD: cat left.fa right.fa > both.fa
815s CMD finished (0 seconds)
815s CMD: touch both.fa.ok
815s CMD finished (0 seconds)
815s -kmer counting.
815s -------------------------------------------
815s ----------- Jellyfish  --------------------
815s -- (building a k-mer catalog from reads) --
815s -------------------------------------------
815s 
815s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
816s CMD finished (1 seconds)
816s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
816s CMD finished (0 seconds)
816s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
816s CMD finished (0 seconds)
816s CMD: touch jellyfish.K25.min2.kmers.fa.success
816s CMD finished (0 seconds)
816s -generating stats files
816s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
816s -reading Kmer occurrences...
816s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
816s -reading Kmer occurrences...
816s 
816s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
816s 
816s  done parsing 88153 Kmers, 88076 added, taking 0 seconds.
817s STATS_GENERATION_TIME: 1 seconds.
817s STATS_GENERATION_TIME: 1 seconds.
817s CMD finished (1 seconds)
817s CMD finished (1 seconds)
817s CMD: touch left.fa.K25.stats.ok
817s CMD finished (0 seconds)
817s CMD: touch right.fa.K25.stats.ok
817s CMD finished (0 seconds)
817s -sorting each stats file by read name.
817s 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
817s 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
817s CMD finished (0 seconds)
817s CMD finished (0 seconds)
817s CMD: touch left.fa.K25.stats.sort.ok
817s CMD finished (0 seconds)
817s CMD: touch right.fa.K25.stats.sort.ok
817s CMD finished (0 seconds)
817s -defining normalized reads
817s 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
817s -opening left.fa.K25.stats.sort
817s -opening right.fa.K25.stats.sort
817s -done opening files.
817s CMD finished (0 seconds)
817s CMD: touch pairs.K25.stats.ok
817s CMD finished (0 seconds)
817s 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
818s 27678 / 27726 = 99.83% reads selected during normalization.
818s 0 / 27726 = 0.00% reads discarded as likely aberrant based on coverage profiles.
818s 0 / 27726 = 0.00% reads discarded as below minimum coverage threshold=1
818s CMD finished (1 seconds)
818s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
818s CMD finished (0 seconds)
818s -search and capture.
818s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/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.
818s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.left.fq.PwU.qtrim.fq
818s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/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.
818s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/reads2.right.fq.PwU.qtrim.fq
818s CMD: touch /tmp/autopkgtest.xkSdGF/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
818s CMD finished (0 seconds)
818s CMD: touch /tmp/autopkgtest.xkSdGF/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
818s CMD finished (0 seconds)
818s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
818s CMD finished (0 seconds)
818s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
818s CMD finished (0 seconds)
818s -removing tmp dir /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/tmp_normalized_reads
818s 
818s 
818s Normalization complete. See outputs: 
818s 	/tmp/autopkgtest.xkSdGF/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
818s 	/tmp/autopkgtest.xkSdGF/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
818s Friday, November 1, 2024: 10:22:13	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/normalization.ok
818s # running normalization on reads: $VAR1 = [
818s           [
818s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq',
818s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq'
818s           ],
818s           [
818s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq',
818s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq'
818s           ]
818s         ];
818s 
818s 
818s Friday, November 1, 2024: 10:22:13	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq,/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq --right /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq,/tmp/autopkgtest.xkSdGF/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  
818s -prepping seqs
818s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq >> left.fa
818s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq >> right.fa
818s CMD finished (0 seconds)
818s CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq >> left.fa
818s CMD finished (0 seconds)
818s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq >> right.fa
818s CMD finished (0 seconds)
818s CMD finished (0 seconds)
818s CMD: touch left.fa.ok
818s CMD finished (0 seconds)
818s CMD: touch right.fa.ok
818s CMD finished (0 seconds)
818s Done converting input files.CMD: cat left.fa right.fa > both.fa
818s CMD finished (0 seconds)
818s CMD: touch both.fa.ok
818s CMD finished (0 seconds)
818s -kmer counting.
818s -------------------------------------------
818s ----------- Jellyfish  --------------------
818s -- (building a k-mer catalog from reads) --
818s -------------------------------------------
818s 
818s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
820s CMD finished (2 seconds)
820s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
820s CMD finished (0 seconds)
820s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
820s CMD finished (0 seconds)
820s CMD: touch jellyfish.K25.min2.kmers.fa.success
820s CMD finished (0 seconds)
820s -generating stats files
820s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
820s -reading Kmer occurrences...
820s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
820s -reading Kmer occurrences...
820s 
820s  done parsing 311705 Kmers, 310319 added, taking 0 seconds.
820s 
820s  done parsing 311705 Kmers, 310319 added, taking 0 seconds.
821s STATS_GENERATION_TIME: 1 seconds.
821s STATS_GENERATION_TIME: 1 seconds.
822s CMD finished (1 seconds)
822s CMD finished (1 seconds)
822s CMD: touch left.fa.K25.stats.ok
822s CMD finished (0 seconds)
822s CMD: touch right.fa.K25.stats.ok
822s CMD finished (0 seconds)
822s -sorting each stats file by read name.
822s 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
822s 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
822s CMD finished (0 seconds)
822s CMD finished (0 seconds)
822s CMD: touch left.fa.K25.stats.sort.ok
822s CMD finished (0 seconds)
822s CMD: touch right.fa.K25.stats.sort.ok
822s CMD finished (0 seconds)
822s -defining normalized reads
822s 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
822s -opening left.fa.K25.stats.sort
822s -opening right.fa.K25.stats.sort
822s -done opening files.
822s CMD finished (0 seconds)
822s CMD: touch pairs.K25.stats.ok
822s CMD finished (0 seconds)
822s 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
823s 51602 / 55356 = 93.22% reads selected during normalization.
823s 0 / 55356 = 0.00% reads discarded as likely aberrant based on coverage profiles.
823s 0 / 55356 = 0.00% reads discarded as below minimum coverage threshold=1
823s CMD finished (1 seconds)
823s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
823s CMD finished (0 seconds)
823s -search and capture.
824s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq /tmp/autopkgtest.xkSdGF/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.
824s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/right.norm.fq
824s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/right.norm.fq
824s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq /tmp/autopkgtest.xkSdGF/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.
824s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_1/left.norm.fq
824s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/norm_for_read_set_2/left.norm.fq
824s CMD: touch /tmp/autopkgtest.xkSdGF/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
824s CMD finished (0 seconds)
824s CMD: touch /tmp/autopkgtest.xkSdGF/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
824s CMD finished (0 seconds)
824s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
824s CMD finished (0 seconds)
824s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
824s CMD finished (0 seconds)
824s -removing tmp dir /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/tmp_normalized_reads
824s 
824s 
824s Normalization complete. See outputs: 
824s 	/tmp/autopkgtest.xkSdGF/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
824s 	/tmp/autopkgtest.xkSdGF/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
824s Friday, November 1, 2024: 10:22:19	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/insilico_read_normalization_altogether/normalization.ok
824s Converting input files. (in parallel)Friday, November 1, 2024: 10:22:19	CMD: cat /tmp/autopkgtest.xkSdGF/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
824s Friday, November 1, 2024: 10:22:19	CMD: cat /tmp/autopkgtest.xkSdGF/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
824s Friday, November 1, 2024: 10:22:19	CMD: touch left.fa.ok
824s Friday, November 1, 2024: 10:22:19	CMD: touch right.fa.ok
824s Friday, November 1, 2024: 10:22:19	CMD: touch left.fa.ok right.fa.ok
824s Friday, November 1, 2024: 10:22:19	CMD: cat left.fa right.fa > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
824s Friday, November 1, 2024: 10:22:19	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa.ok
824s -------------------------------------------
824s ----------- Jellyfish  --------------------
824s -- (building a k-mer (25) catalog from reads) --
824s -------------------------------------------
824s 
824s * [Fri Nov  1 10:22:19 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
826s * [Fri Nov  1 10:22:21 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
826s * [Fri Nov  1 10:22:21 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
826s ----------------------------------------------
826s --------------- Inchworm (K=25, asm) ---------------------
826s -- (Linear contig construction from k-mers) --
826s ----------------------------------------------
826s 
826s * [Fri Nov  1 10:22:21 2024] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --num_threads 2  --PARALLEL_IWORM   --min_any_entropy 1.0   -L 25  --no_prune_error_kmers  > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa.tmp
826s Kmer length set to: 25
826s Min assembly length set to: 25
826s Monitor turned on, set to: 1
826s min entropy set to: 1
826s setting number of threads to: 2
826s -setting parallel iworm mode.
826s -reading Kmer occurrences...
826s 
 [0M] Kmers parsed.     
826s  done parsing 309493 Kmers, 309493 added, taking 0 seconds.
826s 
826s TIMING KMER_DB_BUILDING 0 s.
826s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
826s Pruned 1482 kmers from catalog.
826s 	Pruning time: 0 seconds = 0 minutes.
826s 
826s TIMING PRUNING 0 s.
826s -populating the kmer seed candidate list.
826s Kcounter hash size: 309493
826s Processed 308011 non-zero abundance kmers in kcounter.
826s -Not sorting list of kmers, given parallel mode in effect.
826s -beginning inchworm contig assembly.
826s Total kcounter hash size: 309493 vs. sorted list size: 308011
826s num threads set to: 2
826s Done opening file. tmp.iworm.fa.pid_44005.thread_0
826s Done opening file. tmp.iworm.fa.pid_44005.thread_1
827s 
827s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
827s 
827s TIMING CONTIG_BUILDING 1 s.
827s 
827s TIMING PROG_RUNTIME 1 s.
827s * [Fri Nov  1 10:22:22 2024] Running CMD: mv /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa.tmp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa
827s Friday, November 1, 2024: 10:22:22	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa.finished
827s --------------------------------------------------------
827s -------------------- Chrysalis -------------------------
827s -- (Contig Clustering & de Bruijn Graph Construction) --
827s --------------------------------------------------------
827s 
827s inchworm_target: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
827s bowtie_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
827s chrysalis_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa
827s * [Fri Nov  1 10:22:22 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/inchworm.fa 100 10 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100
827s * [Fri Nov  1 10:22:22 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 1>/dev/null
827s * [Fri Nov  1 10:22:22 2024] Running CMD: bash -c " set -o pipefail;/usr/bin/bowtie2 --local -k 2 --no-unal --threads 2 -f --score-min G,20,8 -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm.bowtie.nameSorted.bam" 
831s * [Fri Nov  1 10:22:26 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_scaffolds.txt
832s * [Fri Nov  1 10:22:27 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt
833s * [Fri Nov  1 10:22:28 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted
833s * [Fri Nov  1 10:22:28 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
833s * [Fri Nov  1 10:22:28 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/GraphFromIwormFasta.out
833s * [Fri Nov  1 10:22:28 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/bundled_iworm_contigs.fasta -min 200
833s * [Fri Nov  1 10:22:28 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa -f /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.xkSdGF/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 
837s * [Fri Nov  1 10:22:32 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/readsToComponents.out > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/chrysalis/readsToComponents.out.sort
837s Friday, November 1, 2024: 10:22:32	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/read_partitions/Fb_0/CBin_0
837s Friday, November 1, 2024: 10:22:32	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/partitioned_reads.files.list.ok
837s Friday, November 1, 2024: 10:22:32	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.xkSdGF/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
838s Friday, November 1, 2024: 10:22:32	CMD: touch recursive_trinity.cmds.ok
838s Friday, November 1, 2024: 10:22:32	CMD: touch recursive_trinity.cmds.ok
838s 
838s 
838s --------------------------------------------------------------------------------
838s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
838s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
838s --------------------------------------------------------------------------------
838s 
838s Friday, November 1, 2024: 10:22:32	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
838s Number of Commands: 51
930s 
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.    
930s 
930s All commands completed successfully. :-)
930s 
930s 
930s 
930s ** Harvesting all assembled transcripts into a single multi-fasta file...
930s 
930s Friday, November 1, 2024: 10:24:05	CMD: find /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/Trinity.tmp
930s * [Fri Nov  1 10:24:05 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa 2
931s * [Fri Nov  1 10:24:06 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta
931s Friday, November 1, 2024: 10:24:06	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta.gene_trans_map
931s 
931s 
931s #############################################################################
931s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_trim_and_norm_outdir.Trinity.fasta
931s #############################################################################
931s 
931s 
931s ./misc_run_tests/__runMe_include_long_reads.sh
931s 
931s 
931s 
931s exit 0
931s #!/bin/bash -ve
931s 
931s #######################################################
931s ##  Run Trinity to Generate Transcriptome Assemblies ##
931s #######################################################
931s 
931s CPU=$(nproc || sysctl -n hw.physicalcpu)
931s 
931s ${TRINITY_HOME}/Trinity --seqType fq \
931s               --max_memory 2G \
931s               --left reads.left.fq.gz \
931s               --right reads.right.fq.gz \
931s               --SS_lib_type RF \
931s               --CPU ${CPU} \
931s               --no_cleanup \
931s               --long_reads longReads.fa \
931s               --output test_trinity_long_reads
931s 
931s 
931s      ______  ____   ____  ____   ____  ______  __ __
931s     |      ||    \ |    ||    \ |    ||      ||  |  |
931s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
931s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
931s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
931s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
931s       |__|  |__|\_||____||__|__||____|  |__|  |____/
931s 
931s     Trinity-v2.15.1
931s 
931s 
931s 
931s Left read files: $VAR1 = [
931s           'reads.left.fq.gz'
931s         ];
931s Right read files: $VAR1 = [
931s           'reads.right.fq.gz'
931s         ];
931s Friday, November 1, 2024: 10:24:06	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads
931s Friday, November 1, 2024: 10:24:06	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis
931s 
931s 
931s ----------------------------------------------------------------------------------
931s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
931s ----------------------------------------------------------------------------------
931s 
931s ---------------------------------------------------------------
931s ------------ In silico Read Normalization ---------------------
931s -- (Removing Excess Reads Beyond 200 Coverage --
931s ---------------------------------------------------------------
931s 
931s # running normalization on reads: $VAR1 = [
931s           [
931s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
931s           ],
931s           [
931s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
931s           ]
931s         ];
931s 
931s 
931s Friday, November 1, 2024: 10:24:06	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together  --PARALLEL_STATS  
931s -prepping seqs
931s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
931s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
931s CMD finished (0 seconds)
931s CMD finished (0 seconds)
931s CMD: touch left.fa.ok
931s CMD finished (0 seconds)
931s CMD: touch right.fa.ok
931s CMD finished (0 seconds)
931s Done converting input files.CMD: cat left.fa right.fa > both.fa
931s CMD finished (0 seconds)
931s CMD: touch both.fa.ok
931s CMD finished (0 seconds)
931s -kmer counting.
931s -------------------------------------------
931s ----------- Jellyfish  --------------------
931s -- (building a k-mer catalog from reads) --
931s -------------------------------------------
931s 
931s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
932s CMD finished (1 seconds)
932s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
932s CMD finished (0 seconds)
932s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
933s CMD finished (0 seconds)
933s CMD: touch jellyfish.K25.min2.kmers.fa.success
933s CMD finished (0 seconds)
933s -generating stats files
933s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
933s -reading Kmer occurrences...
933s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
933s -reading Kmer occurrences...
933s 
933s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
933s 
933s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
933s STATS_GENERATION_TIME: 0 seconds.
933s CMD finished (0 seconds)
933s STATS_GENERATION_TIME: 0 seconds.
933s CMD finished (0 seconds)
933s CMD: touch left.fa.K25.stats.ok
933s CMD finished (0 seconds)
933s CMD: touch right.fa.K25.stats.ok
933s CMD finished (0 seconds)
933s -sorting each stats file by read name.
933s 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
933s 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
933s CMD finished (0 seconds)
933s CMD finished (0 seconds)
933s CMD: touch left.fa.K25.stats.sort.ok
933s CMD finished (0 seconds)
933s CMD: touch right.fa.K25.stats.sort.ok
933s CMD finished (0 seconds)
933s -defining normalized reads
933s 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
933s -opening left.fa.K25.stats.sort
933s -opening right.fa.K25.stats.sort
933s -done opening files.
934s CMD finished (1 seconds)
934s CMD: touch pairs.K25.stats.ok
934s CMD finished (0 seconds)
934s 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
934s 30472 / 30575 = 99.66% reads selected during normalization.
934s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
934s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
934s CMD finished (0 seconds)
934s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
934s CMD finished (0 seconds)
934s -search and capture.
934s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture.
934s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
934s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture.
934s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
935s CMD: touch /tmp/autopkgtest.xkSdGF/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
935s CMD finished (0 seconds)
935s CMD: touch /tmp/autopkgtest.xkSdGF/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
935s CMD finished (0 seconds)
935s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
935s CMD finished (0 seconds)
935s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
935s CMD finished (0 seconds)
935s 
935s 
935s Normalization complete. See outputs: 
935s 	/tmp/autopkgtest.xkSdGF/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
935s 	/tmp/autopkgtest.xkSdGF/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
935s Friday, November 1, 2024: 10:24:10	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/insilico_read_normalization/normalization.ok
935s Converting input files. (in parallel)Friday, November 1, 2024: 10:24:10	CMD: cat /tmp/autopkgtest.xkSdGF/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
935s Friday, November 1, 2024: 10:24:10	CMD: cat /tmp/autopkgtest.xkSdGF/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
935s Friday, November 1, 2024: 10:24:10	CMD: touch left.fa.ok
935s Friday, November 1, 2024: 10:24:10	CMD: touch right.fa.ok
935s Friday, November 1, 2024: 10:24:10	CMD: touch left.fa.ok right.fa.ok
935s Friday, November 1, 2024: 10:24:10	CMD: cat left.fa right.fa > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa
935s Friday, November 1, 2024: 10:24:10	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.ok
935s Friday, November 1, 2024: 10:24:10	CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR
935s Friday, November 1, 2024: 10:24:10	CMD: cat /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/longReads.fa | sed 's/>/>LR\$\|/' >> /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR
935s Friday, November 1, 2024: 10:24:10	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR.ok
935s -------------------------------------------
935s ----------- Jellyfish  --------------------
935s -- (building a k-mer (25) catalog from reads) --
935s -------------------------------------------
935s 
935s * [Fri Nov  1 10:24:10 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa
936s * [Fri Nov  1 10:24:11 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
936s * [Fri Nov  1 10:24:11 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
936s ----------------------------------------------
936s --------------- Inchworm (K=25, asm) ---------------------
936s -- (Linear contig construction from k-mers) --
936s ----------------------------------------------
936s 
936s * [Fri Nov  1 10:24:11 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa.tmp
936s Kmer length set to: 25
936s Min assembly length set to: 25
936s Monitor turned on, set to: 1
936s -retaining tmp files
936s min entropy set to: 1
936s setting number of threads to: 2
936s -setting parallel iworm mode.
936s -reading Kmer occurrences...
937s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
937s  done parsing 519541 Kmers, 519541 added, taking 1 seconds.
937s 
937s TIMING KMER_DB_BUILDING 1 s.
937s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
937s Pruned 4252 kmers from catalog.
937s 	Pruning time: 0 seconds = 0 minutes.
937s 
937s TIMING PRUNING 0 s.
937s -populating the kmer seed candidate list.
937s Kcounter hash size: 519541
937s Processed 515289 non-zero abundance kmers in kcounter.
937s -Not sorting list of kmers, given parallel mode in effect.
937s -beginning inchworm contig assembly.
937s Total kcounter hash size: 519541 vs. sorted list size: 515289
937s num threads set to: 2
937s Done opening file. tmp.iworm.fa.pid_52940.thread_0
937s Done opening file. tmp.iworm.fa.pid_52940.thread_1
938s 
938s 	Iworm contig assembly time: 0 seconds = 0 minutes.
938s 
938s TIMING CONTIG_BUILDING 0 s.
938s 
938s TIMING PROG_RUNTIME 1 s.
938s * [Fri Nov  1 10:24:13 2024] Running CMD: mv /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa.tmp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa
938s Friday, November 1, 2024: 10:24:13	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa.finished
938s --------------------------------------------------------
938s -------------------- Chrysalis -------------------------
938s -- (Contig Clustering & de Bruijn Graph Construction) --
938s --------------------------------------------------------
938s 
938s inchworm_target: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa
938s bowtie_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa
938s chrysalis_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR
938s * [Fri Nov  1 10:24:13 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/inchworm.fa 100 10 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100
938s * [Fri Nov  1 10:24:13 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 1>/dev/null
938s * [Fri Nov  1 10:24:13 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm.bowtie.nameSorted.bam" 
941s * [Fri Nov  1 10:24:16 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_scaffolds.txt
941s * [Fri Nov  1 10:24:16 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt
943s * [Fri Nov  1 10:24:18 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted
943s * [Fri Nov  1 10:24:18 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
943s * [Fri Nov  1 10:24:18 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/GraphFromIwormFasta.out
943s * [Fri Nov  1 10:24:18 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/bundled_iworm_contigs.fasta -min 200
943s * [Fri Nov  1 10:24:18 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa.wLR -f /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -strand  -p 10 
945s * [Fri Nov  1 10:24:20 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/readsToComponents.out > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/chrysalis/readsToComponents.out.sort
946s Friday, November 1, 2024: 10:24:21	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/read_partitions/Fb_0/CBin_0
946s Friday, November 1, 2024: 10:24:21	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/partitioned_reads.files.list.ok
946s Friday, November 1, 2024: 10:24:21	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.xkSdGF/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
946s Friday, November 1, 2024: 10:24:21	CMD: touch recursive_trinity.cmds.ok
946s Friday, November 1, 2024: 10:24:21	CMD: touch recursive_trinity.cmds.ok
946s 
946s 
946s --------------------------------------------------------------------------------
946s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
946s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
946s --------------------------------------------------------------------------------
946s 
946s Friday, November 1, 2024: 10:24:21	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
946s Number of Commands: 39
1006s 
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.    
1006s 
1006s All commands completed successfully. :-)
1006s 
1006s 
1006s 
1006s ** Harvesting all assembled transcripts into a single multi-fasta file...
1006s 
1006s Friday, November 1, 2024: 10:25:21	CMD: find /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/Trinity.tmp
1006s * [Fri Nov  1 10:25:21 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa 2
1007s * [Fri Nov  1 10:25:22 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta
1007s Friday, November 1, 2024: 10:25:22	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta.gene_trans_map
1007s 
1007s 
1007s #############################################################################
1007s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/test_trinity_long_reads.Trinity.fasta
1007s #############################################################################
1007s 
1007s 
1007s 
1007s 
1007s find test_trinity_long_reads/ -regex ".*allProbPaths.fasta"  -exec cat {} \; | grep LR
1007s >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(+)]}
1007s >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$|mm9chr4-NM_010598;mm9chr4-16498_Kcnab2_potassium_voltage-gated_channel,_shaker-related_mm9chr4:151767144-151809990(-)]}
1007s >c0_g1_i3 len=3590 path=[3675:0-117 3770:118-137 265:138-140 268:141-250 3806:251-310 396:311-3589] [-1, 3675, 3770, 265, 268, 3806, 396, -2] long_read_mappings: {PairPath [_paths=[[268, 3806, 396], []]]=[LR$|mm9chr4-NM_010598;mm9chr4-16498_Kcnab2_potassium_voltage-gated_channel,_shaker-related_mm9chr4:151767144-151809990(-)]}
1007s >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$|mm9chr6-NM_022332;mm9chr6-64213_St7_low_density_lipoprotein-related_protein_12_mm9chr6:17699593-17892765(+)]}
1007s >c0_g1_i5 len=2364 path=[1:0-610 589:611-1077 1056:1078-1099 1078:1100-1541 1520:1542-1621 1600:1622-1794 1773:1795-2028 2007:2029-2029 2008:2030-2363] [-1, 1, 589, 1056, 1078, 1520, 1600, 1773, 2007, 2008, -2] long_read_mappings: {PairPath [_paths=[[1, 589, 1056, 1078, 1520, 1600, 1773, 2007, 2008], []]]=[LR$|mm9chr6-NM_001083315;mm9chr6-64213_St7_low_density_lipoprotein-related_protein_12_mm9chr6:17699593-17892765(+)]}
1007s >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$|mm9chr5-NM_172722;mm9chr5-231713_Naa25_Nalpha_acteyltransferase_25_mm9chr5:121848014-121889959(+)]}
1007s >c0_g1_i5 len=5399 path=[1:0-1751 1730:1752-1773 1752:1774-2693 2672:2694-4164 4143:4165-5398] [-1, 1, 1730, 1752, 2672, 4143, -2] long_read_mappings: {PairPath [_paths=[[1, 1730, 1752, 2672], []]]=[LR$|mm9chr5-NM_172722;mm9chr5-231713_Naa25_Nalpha_acteyltransferase_25_mm9chr5:121848014-121889959(+)]}
1007s >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$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]}
1007s >c0_g1_i2 len=2177 path=[2641:0-65 2684:66-412 3031:413-413 3032:414-495 3114:496-2156 8302:2157-2176] [-1, 2641, 2684, 3031, 3032, 3114, 8302, -2] long_read_mappings: {PairPath [_paths=[[3114], []]]=[LR$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]}
1007s >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$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]}
1007s >c0_g1_i4 len=5494 path=[2641:0-65 2684:66-412 3031:413-413 3032:414-495 3114:496-2156 4775:2157-3903 6522:3904-3919 6538:3920-4997 7616:4998-4998 7617:4999-5035 7616:5036-5036 7654:5037-5493] [-1, 2641, 2684, 3031, 3032, 3114, 4775, 6522, 6538, 7616, 7617, 7616, 7654, -2] long_read_mappings: {PairPath [_paths=[[3114], []]]=[LR$|mm9chr3-NM_053182;mm9chr3-94212_Pag1_phosphoprotein_associated_with_glycosphingolipid_mm9chr3:9693767-9706213(-)]}
1007s >c0_g2_i1 len=3966 path=[6618:0-165 147:166-1345 6761:1346-1417 1348:1418-1418 8338:1419-1442 1373:1443-2963 2894:2964-3730 6857:3731-3965] [-1, 6618, 147, 6761, 1348, 8338, 1373, 2894, 6857, -2] long_read_mappings: {PairPath [_paths=[[147, 6761, 1348, 8338, 1373, 2894, 6857], []]]=[LR$|mm9chr7-NM_022979;mm9chr7-269966_Nup98_nucleoporin_98_mm9chr7:109283074-109344374(-)]}
1007s >c0_g1_i1 len=6205 path=[1:0-1805 1784:1806-1822 1801:1823-5597 5576:5598-5738 5717:5739-5739 5718:5740-6173 6152:6174-6203 7380:6204-6204] [-1, 1, 1784, 1801, 5576, 5717, 5718, 6152, 7380, -2] long_read_mappings: {PairPath [_paths=[[1, 1784, 1801, 5576, 5717, 5718], []]]=[LR$|mm9chr1-NM_001102430;mm9chr1-211673_Arfgef1_ADP-ribosylation_factor_guanine_mm9chr1:10128913-10222575(-)]}
1007s >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$|mm9chr1-NM_001102430;mm9chr1-211673_Arfgef1_ADP-ribosylation_factor_guanine_mm9chr1:10128913-10222575(-)]}
1007s >c0_g1_i6 len=7194 path=[1:0-1805 1784:1806-1822 1801:1823-5597 5576:5598-5738 5717:5739-5739 5718:5740-6173 6152:6174-6203 6182:6204-6219 6198:6220-6729 6708:6730-6733 6712:6734-6735 6714:6736-7193] [-1, 1, 1784, 1801, 5576, 5717, 5718, 6152, 6182, 6198, 6708, 6712, 6714, -2] long_read_mappings: {PairPath [_paths=[[1, 1784, 1801, 5576, 5717, 5718], []]]=[LR$|mm9chr1-NM_001102430;mm9chr1-211673_Arfgef1_ADP-ribosylation_factor_guanine_mm9chr1:10128913-10222575(-)]}
1007s >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$|mm9chr8-NM_027590;mm9chr8-70885_Ints10_integrator_complex_subunit_10_mm9chr8:71317919-71351332(+)]}
1007s >c0_g2_i16 len=2273 path=[1:0-1204 1183:1205-1226 1205:1227-1649 1628:1650-1650 6231:1651-1674 1653:1675-2040 2019:2041-2041 2020:2042-2063 2042:2064-2227 2206:2228-2248 6207:2249-2272] [-1, 1, 1183, 1205, 1628, 6231, 1653, 2019, 2020, 2042, 2206, 6207, -2] long_read_mappings: {PairPath [_paths=[[1, 1183, 1205, 1628, 6231, 1653, 2019, 2020, 2042], []]]=[LR$|mm9chr8-NM_027590;mm9chr8-70885_Ints10_integrator_complex_subunit_10_mm9chr8:71317919-71351332(+)]}
1007s >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$|mm9chr2-NM_033134;mm9chr2-64436_Inpp5e_inositol_polyphosphate-5-phosphatase_E_mm9chr2:26253359-26264107(-)]}
1007s >c0_g3_i6 len=7669 path=[1:0-333 312:334-1874 1853:1875-2722 2701:2723-3436 3415:3437-3734 10929:3735-3758 3737:3759-3759 3738:3760-4380 4359:4381-6314 6293:6315-6645 6624:6646-6646 6625:6647-6661 6640:6662-6662 6641:6663-7161 7140:7162-7164 7143:7165-7182 7161:7183-7208 7187:7209-7239 7218:7240-7260 7239:7261-7261 10928:7262-7285 7264:7286-7623 8735:7624-7668] [-1, 1, 312, 1853, 2701, 3415, 10929, 3737, 3738, 4359, 6293, 6624, 6625, 6640, 6641, 7140, 7143, 7161, 7187, 7218, 7239, 10928, 7264, 8735, -2] long_read_mappings: {PairPath [_paths=[[1, 312, 1853, 2701, 3415, 10929, 3737, 3738, 4359, 6293, 6624, 6625, 6640, 6641, 7140, 7143, 7161, 7187, 7218, 7239, 10928, 7264], []]]=[LR$|mm9chr2-NM_153125;mm9chr2-227648_Sec16a_SEC16_homolog_A_mm9chr2:26266405-26297521(-)]}
1007s >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, 109
1007s 29, 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(-)]}
1007s 
1007s exit 0
1007s ./misc_run_tests/__run_PE_samples_file.sh
1007s #!/bin/bash -ve
1007s 
1007s ${TRINITY_HOME}/Trinity --samples_file samples.PE.txt \
1007s               --seqType fq \
1007s               --max_memory 1G \
1007s               --output trinity_test_samples_PE
1007s 
1007s 
1007s      ______  ____   ____  ____   ____  ______  __ __
1007s     |      ||    \ |    ||    \ |    ||      ||  |  |
1007s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1007s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1007s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1007s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1007s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1007s 
1007s     Trinity-v2.15.1
1007s 
1007s 
1007s 
1007s Left read files: $VAR1 = [
1007s           'reads.left.fq.gz',
1007s           'reads2.left.fq.gz'
1007s         ];
1007s Right read files: $VAR1 = [
1007s           'reads.right.fq.gz',
1007s           'reads2.right.fq.gz'
1007s         ];
1007s Friday, November 1, 2024: 10:25:22	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE
1007s Friday, November 1, 2024: 10:25:22	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis
1007s 
1007s 
1007s ----------------------------------------------------------------------------------
1007s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1007s ----------------------------------------------------------------------------------
1007s 
1007s ---------------------------------------------------------------
1007s ------------ In silico Read Normalization ---------------------
1007s -- (Removing Excess Reads Beyond 200 Coverage --
1007s ---------------------------------------------------------------
1007s 
1007s # running normalization on reads: $VAR1 = [
1007s           [
1007s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz',
1007s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz'
1007s           ],
1007s           [
1007s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz',
1007s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz'
1007s           ]
1007s         ];
1007s 
1007s 
1007s Friday, November 1, 2024: 10:25:22	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization --max_CV 10000  --left /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz --right /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz,/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz --pairs_together  --PARALLEL_STATS  
1007s -prepping seqs
1007s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
1007s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
1007s CMD finished (0 seconds)
1007s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz) >> left.fa
1007s CMD finished (0 seconds)
1007s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz) >> right.fa
1007s CMD finished (0 seconds)
1007s CMD finished (0 seconds)
1007s CMD: touch left.fa.ok
1007s CMD finished (0 seconds)
1007s CMD: touch right.fa.ok
1007s CMD finished (0 seconds)
1007s Done converting input files.CMD: cat left.fa right.fa > both.fa
1007s CMD finished (0 seconds)
1007s CMD: touch both.fa.ok
1007s CMD finished (0 seconds)
1007s -kmer counting.
1007s -------------------------------------------
1007s ----------- Jellyfish  --------------------
1007s -- (building a k-mer catalog from reads) --
1007s -------------------------------------------
1007s 
1007s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  both.fa
1009s CMD finished (2 seconds)
1009s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1009s CMD finished (0 seconds)
1009s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1009s CMD finished (0 seconds)
1009s CMD: touch jellyfish.K25.min2.kmers.fa.success
1009s CMD finished (0 seconds)
1009s -generating stats files
1009s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > left.fa.K25.stats
1009s -reading Kmer occurrences...
1009s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > right.fa.K25.stats
1009s -reading Kmer occurrences...
1010s 
1010s  done parsing 518514 Kmers, 518514 added, taking 1 seconds.
1010s 
1010s  done parsing 518514 Kmers, 518514 added, taking 1 seconds.
1011s STATS_GENERATION_TIME: 1 seconds.
1011s STATS_GENERATION_TIME: 1 seconds.
1011s CMD finished (2 seconds)
1011s CMD finished (2 seconds)
1011s CMD: touch left.fa.K25.stats.ok
1011s CMD finished (0 seconds)
1011s CMD: touch right.fa.K25.stats.ok
1011s CMD finished (0 seconds)
1011s -sorting each stats file by read name.
1011s 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
1011s 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
1011s CMD finished (0 seconds)
1011s CMD finished (0 seconds)
1011s CMD: touch left.fa.K25.stats.sort.ok
1011s CMD finished (0 seconds)
1011s CMD: touch right.fa.K25.stats.sort.ok
1011s CMD finished (0 seconds)
1011s -defining normalized reads
1011s 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
1011s -opening left.fa.K25.stats.sort
1011s -opening right.fa.K25.stats.sort
1011s -done opening files.
1012s CMD finished (1 seconds)
1012s CMD: touch pairs.K25.stats.ok
1012s CMD finished (0 seconds)
1012s 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
1013s 56508 / 61150 = 92.41% reads selected during normalization.
1013s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1013s 0 / 61150 = 0.00% reads discarded as below minimum coverage threshold=1
1013s CMD finished (0 seconds)
1013s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
1013s CMD finished (1 seconds)
1013s -search and capture.
1013s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz ... done prepping, now search and capture.
1013s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
1013s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz ... done prepping, now search and capture.
1013s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
1013s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz
1013s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz
1014s CMD: touch /tmp/autopkgtest.xkSdGF/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
1014s CMD finished (0 seconds)
1014s CMD: touch /tmp/autopkgtest.xkSdGF/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
1014s CMD finished (0 seconds)
1014s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
1014s CMD finished (0 seconds)
1014s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
1014s CMD finished (0 seconds)
1014s -removing tmp dir /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/tmp_normalized_reads
1014s 
1014s 
1014s Normalization complete. See outputs: 
1014s 	/tmp/autopkgtest.xkSdGF/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
1014s 	/tmp/autopkgtest.xkSdGF/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
1014s Friday, November 1, 2024: 10:25:29	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/insilico_read_normalization/normalization.ok
1014s Converting input files. (in parallel)Friday, November 1, 2024: 10:25:29	CMD: cat /tmp/autopkgtest.xkSdGF/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
1014s Friday, November 1, 2024: 10:25:29	CMD: cat /tmp/autopkgtest.xkSdGF/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
1014s Friday, November 1, 2024: 10:25:29	CMD: touch left.fa.ok
1014s Friday, November 1, 2024: 10:25:29	CMD: touch right.fa.ok
1014s Friday, November 1, 2024: 10:25:29	CMD: touch left.fa.ok right.fa.ok
1014s Friday, November 1, 2024: 10:25:29	CMD: cat left.fa right.fa > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
1014s Friday, November 1, 2024: 10:25:29	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa.ok
1014s -------------------------------------------
1014s ----------- Jellyfish  --------------------
1014s -- (building a k-mer (25) catalog from reads) --
1014s -------------------------------------------
1014s 
1014s * [Fri Nov  1 10:25:29 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
1016s * [Fri Nov  1 10:25:31 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
1016s * [Fri Nov  1 10:25:31 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
1016s ----------------------------------------------
1016s --------------- Inchworm (K=25, asm) ---------------------
1016s -- (Linear contig construction from k-mers) --
1016s ----------------------------------------------
1016s 
1016s * [Fri Nov  1 10:25:31 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa.tmp
1016s Kmer length set to: 25
1016s Min assembly length set to: 25
1016s Monitor turned on, set to: 1
1016s double stranded mode set
1016s min entropy set to: 1
1016s setting number of threads to: 2
1016s -setting parallel iworm mode.
1016s -reading Kmer occurrences...
1016s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
1016s  done parsing 515206 Kmers, 515206 added, taking 0 seconds.
1016s 
1016s TIMING KMER_DB_BUILDING 0 s.
1016s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
1016s Pruned 4139 kmers from catalog.
1016s 	Pruning time: 0 seconds = 0 minutes.
1016s 
1016s TIMING PRUNING 0 s.
1016s -populating the kmer seed candidate list.
1016s Kcounter hash size: 515206
1016s Processed 511067 non-zero abundance kmers in kcounter.
1016s -Not sorting list of kmers, given parallel mode in effect.
1016s -beginning inchworm contig assembly.
1016s Total kcounter hash size: 515206 vs. sorted list size: 511067
1016s num threads set to: 2
1016s Done opening file. tmp.iworm.fa.pid_60074.thread_0
1016s Done opening file. tmp.iworm.fa.pid_60074.thread_1
1017s 
1017s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
1017s 
1017s TIMING CONTIG_BUILDING 1 s.
1017s 
1017s TIMING PROG_RUNTIME 1 s.
1017s * [Fri Nov  1 10:25:32 2024] Running CMD: mv /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa.tmp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa
1018s Friday, November 1, 2024: 10:25:32	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa.finished
1018s --------------------------------------------------------
1018s -------------------- Chrysalis -------------------------
1018s -- (Contig Clustering & de Bruijn Graph Construction) --
1018s --------------------------------------------------------
1018s 
1018s inchworm_target: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
1018s bowtie_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
1018s chrysalis_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa
1018s * [Fri Nov  1 10:25:32 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/inchworm.DS.fa 100 10 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100
1018s * [Fri Nov  1 10:25:33 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 1>/dev/null
1018s * [Fri Nov  1 10:25:33 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm.bowtie.nameSorted.bam" 
1024s * [Fri Nov  1 10:25:39 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_scaffolds.txt
1025s * [Fri Nov  1 10:25:40 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt
1028s * [Fri Nov  1 10:25:43 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G  -k9,9gr /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted
1028s * [Fri Nov  1 10:25:43 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1028s * [Fri Nov  1 10:25:43 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/inchworm.DS.fa.min100  -weld_graph /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/GraphFromIwormFasta.out
1028s * [Fri Nov  1 10:25:43 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/bundled_iworm_contigs.fasta -min 200
1028s * [Fri Nov  1 10:25:43 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa -f /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -p 10 
1036s * [Fri Nov  1 10:25:51 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/readsToComponents.out > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/chrysalis/readsToComponents.out.sort
1036s Friday, November 1, 2024: 10:25:51	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/read_partitions/Fb_0/CBin_0
1036s Friday, November 1, 2024: 10:25:51	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/partitioned_reads.files.list.ok
1036s Friday, November 1, 2024: 10:25:51	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.xkSdGF/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
1036s Friday, November 1, 2024: 10:25:51	CMD: touch recursive_trinity.cmds.ok
1036s Friday, November 1, 2024: 10:25:51	CMD: touch recursive_trinity.cmds.ok
1036s 
1036s 
1036s --------------------------------------------------------------------------------
1036s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1036s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1036s --------------------------------------------------------------------------------
1036s 
1036s Friday, November 1, 2024: 10:25:51	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
1036s Number of Commands: 63
1151s 
succeeded(1)   1.5873% completed.    
succeeded(2)   3.1746% completed.    
succeeded(3)   4.7619% completed.    
succeeded(4)   6.34921% completed.    
succeeded(5)   7.93651% completed.    
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succeeded(63)   100% completed.    
1151s 
1151s All commands completed successfully. :-)
1151s 
1151s 
1151s 
1151s ** Harvesting all assembled transcripts into a single multi-fasta file...
1151s 
1151s Friday, November 1, 2024: 10:27:46	CMD: find /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/Trinity.tmp
1151s * [Fri Nov  1 10:27:46 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa 2
1153s * [Fri Nov  1 10:27:48 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta
1153s Friday, November 1, 2024: 10:27:48	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta.gene_trans_map
1153s 
1153s 
1153s #############################################################################
1153s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE.Trinity.fasta
1153s #############################################################################
1153s 
1153s 
1153s 
1153s exit 0
1153s ./misc_run_tests/__run_SE_samples_file.sh
1153s #!/bin/bash -ve
1153s 
1153s ${TRINITY_HOME}/Trinity --samples_file samples.SE.txt \
1153s               --seqType fq \
1153s               --max_memory 1G \
1153s               --output trinity_test_samples_SE
1153s 
1153s 
1153s      ______  ____   ____  ____   ____  ______  __ __
1153s     |      ||    \ |    ||    \ |    ||      ||  |  |
1153s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1153s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1153s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1153s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1153s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1153s 
1153s     Trinity-v2.15.1
1153s 
1153s 
1153s 
1153s Single read files: $VAR1 = [
1153s           'reads.left.fq.gz',
1153s           'reads2.left.fq.gz'
1153s         ];
1153s Friday, November 1, 2024: 10:27:48	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE
1153s Friday, November 1, 2024: 10:27:48	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis
1153s 
1153s 
1153s ----------------------------------------------------------------------------------
1153s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1153s ----------------------------------------------------------------------------------
1153s 
1153s ---------------------------------------------------------------
1153s ------------ In silico Read Normalization ---------------------
1153s -- (Removing Excess Reads Beyond 200 Coverage --
1153s ---------------------------------------------------------------
1153s 
1153s # running normalization on reads: $VAR1 = [
1153s           [
1153s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz',
1153s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz'
1153s           ]
1153s         ];
1153s 
1153s 
1153s Friday, November 1, 2024: 10:27:48	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization --max_CV 10000  --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz
1153s -prepping seqs
1153s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> single.fa
1153s CMD finished (0 seconds)
1153s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz) >> single.fa
1153s CMD finished (0 seconds)
1153s CMD: touch single.fa.ok
1153s CMD finished (0 seconds)
1153s -kmer counting.
1153s -------------------------------------------
1153s ----------- Jellyfish  --------------------
1153s -- (building a k-mer catalog from reads) --
1153s -------------------------------------------
1153s 
1153s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  single.fa
1155s CMD finished (2 seconds)
1155s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1155s CMD finished (0 seconds)
1155s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1155s CMD finished (0 seconds)
1155s CMD: touch jellyfish.K25.min2.kmers.fa.success
1155s CMD finished (0 seconds)
1155s -generating stats files
1155s CMD: /usr/bin/fastaToKmerCoverageStats --reads single.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > single.fa.K25.stats
1155s -reading Kmer occurrences...
1155s 
1155s  done parsing 288470 Kmers, 288470 added, taking 0 seconds.
1156s STATS_GENERATION_TIME: 1 seconds.
1156s CMD finished (1 seconds)
1156s CMD: touch single.fa.K25.stats.ok
1156s CMD finished (0 seconds)
1156s -sorting each stats file by read name.
1156s 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
1156s CMD finished (0 seconds)
1156s CMD: touch single.fa.K25.stats.sort.ok
1156s CMD finished (0 seconds)
1156s -defining normalized reads
1156s 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
1156s 59311 / 61150 = 96.99% reads selected during normalization.
1156s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1156s 0 / 61150 = 0.00% reads discarded as below minimum coverage threshold=1
1156s CMD finished (0 seconds)
1156s CMD: touch single.fa.K25.stats.sort.maxC200.minC1.maxCV10000.accs.ok
1156s CMD finished (0 seconds)
1156s -search and capture.
1156s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz ... done prepping, now search and capture.
1156s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
1157s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz
1157s CMD: touch /tmp/autopkgtest.xkSdGF/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
1158s CMD finished (0 seconds)
1158s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
1158s CMD finished (0 seconds)
1158s -removing tmp dir /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/tmp_normalized_reads
1158s 
1158s 
1158s Normalization complete. See outputs: 
1158s 	/tmp/autopkgtest.xkSdGF/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
1158s Friday, November 1, 2024: 10:27:53	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/insilico_read_normalization/normalization.ok
1158s Friday, November 1, 2024: 10:27:53	CMD: cat /tmp/autopkgtest.xkSdGF/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
1158s Friday, November 1, 2024: 10:27:53	CMD: touch single.fa.ok
1158s Friday, November 1, 2024: 10:27:53	CMD: touch single.fa.ok
1158s -------------------------------------------
1158s ----------- Jellyfish  --------------------
1158s -- (building a k-mer (25) catalog from reads) --
1158s -------------------------------------------
1158s 
1158s * [Fri Nov  1 10:27:53 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa
1159s * [Fri Nov  1 10:27:54 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
1159s * [Fri Nov  1 10:27:54 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
1159s ----------------------------------------------
1159s --------------- Inchworm (K=25, asm) ---------------------
1159s -- (Linear contig construction from k-mers) --
1159s ----------------------------------------------
1159s 
1159s * [Fri Nov  1 10:27:54 2024] Running CMD: /usr/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --DS  --num_threads 2  --PARALLEL_IWORM   --min_any_entropy 1.0   -L 25  --no_prune_error_kmers  > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa.tmp
1159s Kmer length set to: 25
1159s Min assembly length set to: 25
1159s Monitor turned on, set to: 1
1159s double stranded mode set
1159s min entropy set to: 1
1159s setting number of threads to: 2
1159s -setting parallel iworm mode.
1159s -reading Kmer occurrences...
1159s 
 [0M] Kmers parsed.     
1159s  done parsing 287930 Kmers, 287930 added, taking 0 seconds.
1159s 
1159s TIMING KMER_DB_BUILDING 0 s.
1159s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
1159s Pruned 2078 kmers from catalog.
1159s 	Pruning time: 0 seconds = 0 minutes.
1159s 
1159s TIMING PRUNING 0 s.
1159s -populating the kmer seed candidate list.
1159s Kcounter hash size: 287930
1159s Processed 285852 non-zero abundance kmers in kcounter.
1159s -Not sorting list of kmers, given parallel mode in effect.
1159s -beginning inchworm contig assembly.
1159s Total kcounter hash size: 287930 vs. sorted list size: 285852
1159s num threads set to: 2
1159s Done opening file. tmp.iworm.fa.pid_70579.thread_0
1159s Done opening file. tmp.iworm.fa.pid_70579.thread_1
1160s 
1160s 	Iworm contig assembly time: 1 seconds = 0.0166667 minutes.
1160s 
1160s TIMING CONTIG_BUILDING 1 s.
1160s 
1160s TIMING PROG_RUNTIME 1 s.
1160s * [Fri Nov  1 10:27:55 2024] Running CMD: mv /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa.tmp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa
1160s Friday, November 1, 2024: 10:27:55	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa.finished
1160s --------------------------------------------------------
1160s -------------------- Chrysalis -------------------------
1160s -- (Contig Clustering & de Bruijn Graph Construction) --
1160s --------------------------------------------------------
1160s 
1160s inchworm_target: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa
1160s bowtie_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa
1160s chrysalis_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa
1160s * [Fri Nov  1 10:27:55 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/inchworm.DS.fa 100 10 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100
1160s * [Fri Nov  1 10:27:55 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt
1163s * [Fri Nov  1 10:27:58 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G  -k9,9gr /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted
1163s * [Fri Nov  1 10:27:58 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1163s * [Fri Nov  1 10:27:58 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/inchworm.DS.fa.min100  -weld_graph /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/GraphFromIwormFasta.out
1163s * [Fri Nov  1 10:27:58 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/bundled_iworm_contigs.fasta -min 200
1163s * [Fri Nov  1 10:27:58 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa -f /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -p 10 
1166s * [Fri Nov  1 10:28:01 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/readsToComponents.out > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/chrysalis/readsToComponents.out.sort
1167s Friday, November 1, 2024: 10:28:02	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/read_partitions/Fb_0/CBin_0
1167s Friday, November 1, 2024: 10:28:02	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/partitioned_reads.files.list.ok
1167s Friday, November 1, 2024: 10:28:02	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.xkSdGF/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
1167s Friday, November 1, 2024: 10:28:02	CMD: touch recursive_trinity.cmds.ok
1167s Friday, November 1, 2024: 10:28:02	CMD: touch recursive_trinity.cmds.ok
1167s 
1167s 
1167s --------------------------------------------------------------------------------
1167s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1167s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1167s --------------------------------------------------------------------------------
1167s 
1167s Friday, November 1, 2024: 10:28:02	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
1167s Number of Commands: 45
1238s 
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.    
1238s 
1238s All commands completed successfully. :-)
1238s 
1238s 
1238s 
1238s ** Harvesting all assembled transcripts into a single multi-fasta file...
1238s 
1238s Friday, November 1, 2024: 10:29:13	CMD: find /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/Trinity.tmp
1238s * [Fri Nov  1 10:29:13 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa 2
1239s * [Fri Nov  1 10:29:14 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE/single.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta
1239s Friday, November 1, 2024: 10:29:14	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta.gene_trans_map
1239s 
1239s 
1239s #############################################################################
1239s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_SE.Trinity.fasta
1239s #############################################################################
1239s 
1239s 
1239s ./misc_run_tests/__runMe_use_workdir.sh
1239s 
1239s 
1239s exit 0
1239s #!/bin/bash -ve
1239s 
1239s 
1239s if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
1239s     gunzip -c reads.right.fq.gz > reads.right.fq
1239s fi
1239s 
1239s if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
1239s     gunzip -c reads.left.fq.gz > reads.left.fq
1239s fi
1239s 
1239s 
1239s 
1239s #######################################################
1239s ##  Run Trinity to Generate Transcriptome Assemblies ##
1239s #######################################################
1239s 
1239s CPU=$(nproc || sysctl -n hw.physicalcpu)
1239s 
1239s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \
1239s               --left reads.left.fq \
1239s               --right reads.right.fq \
1239s               --SS_lib_type RF \
1239s               --CPU ${CPU}\
1239s               --output trinity_with_workdir \
1239s               --workdir  /tmp/trinity.workdir.$$ --full_cleanup
1239s 
1239s 
1239s      ______  ____   ____  ____   ____  ______  __ __
1239s     |      ||    \ |    ||    \ |    ||      ||  |  |
1239s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1239s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1239s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1239s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1239s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1239s 
1239s     Trinity-v2.15.1
1239s 
1239s 
1239s 
1239s Left read files: $VAR1 = [
1239s           'reads.left.fq'
1239s         ];
1239s Right read files: $VAR1 = [
1239s           'reads.right.fq'
1239s         ];
1239s Friday, November 1, 2024: 10:29:14	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir
1239s Friday, November 1, 2024: 10:29:14	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis
1239s 
1239s 
1239s ----------------------------------------------------------------------------------
1239s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1239s ----------------------------------------------------------------------------------
1239s 
1239s ---------------------------------------------------------------
1239s ------------ In silico Read Normalization ---------------------
1239s -- (Removing Excess Reads Beyond 200 Coverage --
1239s ---------------------------------------------------------------
1239s 
1239s # running normalization on reads: $VAR1 = [
1239s           [
1239s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq'
1239s           ],
1239s           [
1239s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq'
1239s           ]
1239s         ];
1239s 
1239s 
1239s Friday, November 1, 2024: 10:29:14	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization --max_CV 10000  --SS_lib_type RF  --left /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq --right /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq --pairs_together  --PARALLEL_STATS  
1239s -prepping seqs
1239s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq >> left.fa
1239s CMD: seqtk-trinity seq -A -R 2  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq >> right.fa
1239s CMD finished (0 seconds)
1239s CMD finished (0 seconds)
1239s CMD: touch left.fa.ok
1239s CMD finished (0 seconds)
1239s CMD: touch right.fa.ok
1239s CMD finished (0 seconds)
1239s Done converting input files.CMD: cat left.fa right.fa > both.fa
1239s CMD finished (0 seconds)
1239s CMD: touch both.fa.ok
1239s CMD finished (0 seconds)
1239s -kmer counting.
1239s -------------------------------------------
1239s ----------- Jellyfish  --------------------
1239s -- (building a k-mer catalog from reads) --
1239s -------------------------------------------
1239s 
1239s CMD: jellyfish count -t 2 -m 25 -s 100000000  both.fa
1241s CMD finished (2 seconds)
1241s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1241s CMD finished (0 seconds)
1241s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1241s CMD finished (0 seconds)
1241s CMD: touch jellyfish.K25.min2.kmers.fa.success
1241s CMD finished (0 seconds)
1241s -generating stats files
1241s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > left.fa.K25.stats
1241s -reading Kmer occurrences...
1241s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  > right.fa.K25.stats
1241s -reading Kmer occurrences...
1241s 
1241s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
1241s 
1241s  done parsing 100973 Kmers, 100873 added, taking 0 seconds.
1242s STATS_GENERATION_TIME: 1 seconds.
1242s CMD finished (1 seconds)
1242s STATS_GENERATION_TIME: 1 seconds.
1242s CMD finished (1 seconds)
1242s CMD: touch left.fa.K25.stats.ok
1242s CMD finished (0 seconds)
1242s CMD: touch right.fa.K25.stats.ok
1242s CMD finished (0 seconds)
1242s -sorting each stats file by read name.
1242s 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
1242s 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
1242s CMD finished (0 seconds)
1242s CMD finished (0 seconds)
1242s CMD: touch left.fa.K25.stats.sort.ok
1242s CMD finished (0 seconds)
1242s CMD: touch right.fa.K25.stats.sort.ok
1242s CMD finished (0 seconds)
1242s -defining normalized reads
1242s 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
1242s -opening left.fa.K25.stats.sort
1242s -opening right.fa.K25.stats.sort
1242s -done opening files.
1242s CMD finished (0 seconds)
1242s CMD: touch pairs.K25.stats.ok
1242s CMD finished (0 seconds)
1242s 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
1243s 30472 / 30575 = 99.66% reads selected during normalization.
1243s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1243s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
1243s CMD finished (1 seconds)
1243s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
1243s CMD finished (0 seconds)
1243s -search and capture.
1243s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq ... done prepping, now search and capture.
1243s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq
1243s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq ... done prepping, now search and capture.
1243s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq
1243s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.left.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
1243s CMD finished (0 seconds)
1243s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.right.fq.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
1243s CMD finished (0 seconds)
1243s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
1243s CMD finished (0 seconds)
1243s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
1243s CMD finished (0 seconds)
1243s -removing tmp dir /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/tmp_normalized_reads
1243s 
1243s 
1243s Normalization complete. See outputs: 
1243s 	/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.left.fq.normalized_K25_maxC200_minC1_maxCV10000.fq
1243s 	/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/reads.right.fq.normalized_K25_maxC200_minC1_maxCV10000.fq
1243s Friday, November 1, 2024: 10:29:18	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/insilico_read_normalization/normalization.ok
1243s Converting input files. (in parallel)Friday, November 1, 2024: 10:29:18	CMD: cat /tmp/autopkgtest.xkSdGF/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
1243s Friday, November 1, 2024: 10:29:18	CMD: cat /tmp/autopkgtest.xkSdGF/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
1243s Friday, November 1, 2024: 10:29:18	CMD: touch left.fa.ok
1243s Friday, November 1, 2024: 10:29:18	CMD: touch right.fa.ok
1243s Friday, November 1, 2024: 10:29:18	CMD: touch left.fa.ok right.fa.ok
1243s Friday, November 1, 2024: 10:29:18	CMD: cat left.fa right.fa > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
1243s Friday, November 1, 2024: 10:29:18	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa.ok
1243s -------------------------------------------
1243s ----------- Jellyfish  --------------------
1243s -- (building a k-mer (25) catalog from reads) --
1243s -------------------------------------------
1243s 
1243s * [Fri Nov  1 10:29:18 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
1245s * [Fri Nov  1 10:29:20 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
1245s * [Fri Nov  1 10:29:20 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
1245s ----------------------------------------------
1245s --------------- Inchworm (K=25, asm) ---------------------
1245s -- (Linear contig construction from k-mers) --
1245s ----------------------------------------------
1245s 
1245s * [Fri Nov  1 10:29:20 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa.tmp
1245s Kmer length set to: 25
1245s Min assembly length set to: 25
1245s Monitor turned on, set to: 1
1245s min entropy set to: 1
1245s setting number of threads to: 2
1245s -setting parallel iworm mode.
1245s -reading Kmer occurrences...
1245s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
1245s  done parsing 519541 Kmers, 519541 added, taking 0 seconds.
1245s 
1245s TIMING KMER_DB_BUILDING 0 s.
1245s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
1246s Pruned 4252 kmers from catalog.
1246s 	Pruning time: 1 seconds = 0.0166667 minutes.
1246s 
1246s TIMING PRUNING 1 s.
1246s -populating the kmer seed candidate list.
1246s Kcounter hash size: 519541
1246s Processed 515289 non-zero abundance kmers in kcounter.
1246s -Not sorting list of kmers, given parallel mode in effect.
1246s -beginning inchworm contig assembly.
1246s Total kcounter hash size: 519541 vs. sorted list size: 515289
1246s num threads set to: 2
1246s Done opening file. tmp.iworm.fa.pid_77506.thread_0
1246s Done opening file. tmp.iworm.fa.pid_77506.thread_1
1246s 
1246s 	Iworm contig assembly time: 0 seconds = 0 minutes.
1246s 
1246s TIMING CONTIG_BUILDING 0 s.
1246s 
1246s TIMING PROG_RUNTIME 1 s.
1246s * [Fri Nov  1 10:29:21 2024] Running CMD: mv /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa.tmp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa
1246s Friday, November 1, 2024: 10:29:21	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa.finished
1246s --------------------------------------------------------
1246s -------------------- Chrysalis -------------------------
1246s -- (Contig Clustering & de Bruijn Graph Construction) --
1246s --------------------------------------------------------
1246s 
1246s inchworm_target: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
1246s bowtie_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
1246s chrysalis_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa
1246s * [Fri Nov  1 10:29:21 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/inchworm.fa 100 10 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100
1246s * [Fri Nov  1 10:29:21 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 1>/dev/null
1246s * [Fri Nov  1 10:29:21 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm.bowtie.nameSorted.bam" 
1249s * [Fri Nov  1 10:29:24 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_scaffolds.txt
1250s * [Fri Nov  1 10:29:25 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 -r /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt
1252s * [Fri Nov  1 10:29:27 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted
1252s * [Fri Nov  1 10:29:27 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1252s * [Fri Nov  1 10:29:27 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/inchworm.fa.min100  -weld_graph /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/GraphFromIwormFasta.out
1252s * [Fri Nov  1 10:29:27 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/bundled_iworm_contigs.fasta -min 200
1252s * [Fri Nov  1 10:29:27 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa -f /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -strand  -p 10 
1254s * [Fri Nov  1 10:29:29 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/readsToComponents.out > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/chrysalis/readsToComponents.out.sort
1254s Friday, November 1, 2024: 10:29:29	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/read_partitions/Fb_0/CBin_0
1254s Friday, November 1, 2024: 10:29:29	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/partitioned_reads.files.list.ok
1254s Friday, November 1, 2024: 10:29:29	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.xkSdGF/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.77367  --no_salmon  > recursive_trinity.cmds
1254s Friday, November 1, 2024: 10:29:29	CMD: touch recursive_trinity.cmds.ok
1254s Friday, November 1, 2024: 10:29:29	CMD: touch recursive_trinity.cmds.ok
1254s 
1254s 
1254s --------------------------------------------------------------------------------
1254s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1254s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1254s --------------------------------------------------------------------------------
1254s 
1254s Friday, November 1, 2024: 10:29:29	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
1254s Number of Commands: 38
1320s 
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.    
1320s 
1320s All commands completed successfully. :-)
1320s 
1320s 
1320s 
1320s ** Harvesting all assembled transcripts into a single multi-fasta file...
1320s 
1320s Friday, November 1, 2024: 10:30:35	CMD: find /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/Trinity.tmp
1320s * [Fri Nov  1 10:30:35 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa 2
1321s * [Fri Nov  1 10:30:36 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta
1321s 
1321s 
1321s #############################################################################
1321s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta
1321s #############################################################################
1321s 
1321s 
1321s Friday, November 1, 2024: 10:30:36	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_with_workdir.Trinity.fasta.gene_trans_map
1321s 
1321s 
1321s exit 0
1321s ./misc_run_tests/__runMe_piecemeal.sh
1321s #!/bin/bash -ve
1321s 
1321s #######################################################
1321s ##  Run Trinity to Generate Transcriptome Assemblies ##
1321s #######################################################
1321s 
1321s CPU=$(nproc || sysctl -n hw.physicalcpu)
1321s 
1321s # stop before inchworm (just in silico norm)
1321s ${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
1322s 
1322s 
1322s      ______  ____   ____  ____   ____  ______  __ __
1322s     |      ||    \ |    ||    \ |    ||      ||  |  |
1322s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1322s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1322s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1322s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1322s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1322s 
1322s     Trinity-v2.15.1
1322s 
1322s 
1322s 
1322s Left read files: $VAR1 = [
1322s           'reads.left.fq.gz'
1322s         ];
1322s Right read files: $VAR1 = [
1322s           'reads.right.fq.gz'
1322s         ];
1322s Friday, November 1, 2024: 10:30:37	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal
1322s Friday, November 1, 2024: 10:30:37	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis
1322s 
1322s 
1322s ----------------------------------------------------------------------------------
1322s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1322s ----------------------------------------------------------------------------------
1322s 
1322s ---------------------------------------------------------------
1322s ------------ In silico Read Normalization ---------------------
1322s -- (Removing Excess Reads Beyond 200 Coverage --
1322s ---------------------------------------------------------------
1322s 
1322s # running normalization on reads: $VAR1 = [
1322s           [
1322s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
1322s           ],
1322s           [
1322s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
1322s           ]
1322s         ];
1322s 
1322s 
1322s Friday, November 1, 2024: 10:30:37	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 200 --min_cov 1 --CPU 2 --output /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization --max_CV 10000  --left /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz --right /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz --pairs_together  --PARALLEL_STATS  
1322s -prepping seqs
1322s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
1322s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
1322s CMD finished (0 seconds)
1322s CMD finished (0 seconds)
1322s CMD: touch left.fa.ok
1322s CMD finished (0 seconds)
1322s CMD: touch right.fa.ok
1322s CMD finished (0 seconds)
1322s Done converting input files.CMD: cat left.fa right.fa > both.fa
1322s CMD finished (0 seconds)
1322s CMD: touch both.fa.ok
1322s CMD finished (0 seconds)
1322s -kmer counting.
1322s -------------------------------------------
1322s ----------- Jellyfish  --------------------
1322s -- (building a k-mer catalog from reads) --
1322s -------------------------------------------
1322s 
1322s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  both.fa
1323s CMD finished (1 seconds)
1323s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1323s CMD finished (0 seconds)
1323s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1323s CMD finished (0 seconds)
1323s CMD: touch jellyfish.K25.min2.kmers.fa.success
1323s CMD finished (0 seconds)
1323s -generating stats files
1323s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > left.fa.K25.stats
1323s -reading Kmer occurrences...
1323s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > right.fa.K25.stats
1323s -reading Kmer occurrences...
1323s 
1323s  done parsing 100964 Kmers, 100964 added, taking 0 seconds.
1323s 
1323s  done parsing 100964 Kmers, 100964 added, taking 0 seconds.
1324s STATS_GENERATION_TIME: 1 seconds.
1324s CMD finished (1 seconds)
1324s STATS_GENERATION_TIME: 1 seconds.
1324s CMD finished (1 seconds)
1324s CMD: touch left.fa.K25.stats.ok
1324s CMD finished (0 seconds)
1324s CMD: touch right.fa.K25.stats.ok
1324s CMD finished (0 seconds)
1324s -sorting each stats file by read name.
1324s 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
1324s 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
1324s CMD finished (0 seconds)
1324s CMD finished (0 seconds)
1324s CMD: touch left.fa.K25.stats.sort.ok
1324s CMD finished (0 seconds)
1324s CMD: touch right.fa.K25.stats.sort.ok
1324s CMD finished (0 seconds)
1324s -defining normalized reads
1324s 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
1324s -opening left.fa.K25.stats.sort
1324s -opening right.fa.K25.stats.sort
1324s -done opening files.
1324s CMD finished (0 seconds)
1324s CMD: touch pairs.K25.stats.ok
1324s CMD finished (0 seconds)
1324s 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
1325s 30472 / 30575 = 99.66% reads selected during normalization.
1325s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1325s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=1
1325s CMD finished (1 seconds)
1325s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
1325s CMD finished (0 seconds)
1325s -search and capture.
1325s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz ... done prepping, now search and capture.
1325s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
1325s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz ... done prepping, now search and capture.
1325s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
1325s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
1325s CMD finished (0 seconds)
1325s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
1325s CMD finished (0 seconds)
1325s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
1325s CMD finished (0 seconds)
1325s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
1325s CMD finished (0 seconds)
1325s -removing tmp dir /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/tmp_normalized_reads
1325s 
1325s 
1325s Normalization complete. See outputs: 
1325s 	/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.left.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
1325s 	/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/reads.right.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
1326s Friday, November 1, 2024: 10:30:40	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/normalization.ok
1326s Converting input files. (in parallel)Friday, November 1, 2024: 10:30:40	CMD: cat /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -A -R 1 - >> left.fa
1326s Friday, November 1, 2024: 10:30:41	CMD: cat /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa
1326s Friday, November 1, 2024: 10:30:41	CMD: touch left.fa.ok
1326s Friday, November 1, 2024: 10:30:41	CMD: touch right.fa.ok
1326s Friday, November 1, 2024: 10:30:41	CMD: touch left.fa.ok right.fa.ok
1326s Friday, November 1, 2024: 10:30:41	CMD: cat left.fa right.fa > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1326s Friday, November 1, 2024: 10:30:41	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa.ok
1326s WARNING:  --no_run_inchworm parameter in effect.  Stopping here prior to running inchworm.
1326s 
1326s # stop before chrysalis
1326s ${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
1326s 
1326s 
1326s      ______  ____   ____  ____   ____  ______  __ __
1326s     |      ||    \ |    ||    \ |    ||      ||  |  |
1326s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1326s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1326s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1326s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1326s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1326s 
1326s     Trinity-v2.15.1
1326s 
1326s 
1326s 
1326s Left read files: $VAR1 = [
1326s           'reads.left.fq.gz'
1326s         ];
1326s Right read files: $VAR1 = [
1326s           'reads.right.fq.gz'
1326s         ];
1326s 
1326s 
1326s ----------------------------------------------------------------------------------
1326s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1326s ----------------------------------------------------------------------------------
1326s 
1326s ---------------------------------------------------------------
1326s ------------ In silico Read Normalization ---------------------
1326s -- (Removing Excess Reads Beyond 200 Coverage --
1326s ---------------------------------------------------------------
1326s 
1326s # running normalization on reads: $VAR1 = [
1326s           [
1326s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
1326s           ],
1326s           [
1326s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
1326s           ]
1326s         ];
1326s 
1326s 
1326s -------------------------------------------
1326s ----------- Jellyfish  --------------------
1326s -- (building a k-mer (25) catalog from reads) --
1326s -------------------------------------------
1326s 
1326s * [Fri Nov  1 10:30:41 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1327s * [Fri Nov  1 10:30:42 2024] Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
1327s * [Fri Nov  1 10:30:42 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
1327s ----------------------------------------------
1327s --------------- Inchworm (K=25, asm) ---------------------
1327s -- (Linear contig construction from k-mers) --
1327s ----------------------------------------------
1327s 
1327s * [Fri Nov  1 10:30:42 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa.tmp
1327s Kmer length set to: 25
1327s Min assembly length set to: 25
1327s Monitor turned on, set to: 1
1327s double stranded mode set
1327s min entropy set to: 1
1327s setting number of threads to: 2
1327s -setting parallel iworm mode.
1327s -reading Kmer occurrences...
1328s 
 [0M] Kmers parsed.     
 [0M] Kmers parsed.     
1328s  done parsing 517949 Kmers, 517949 added, taking 1 seconds.
1328s 
1328s TIMING KMER_DB_BUILDING 1 s.
1328s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
1328s Pruned 4114 kmers from catalog.
1328s 	Pruning time: 0 seconds = 0 minutes.
1328s 
1328s TIMING PRUNING 0 s.
1328s -populating the kmer seed candidate list.
1328s Kcounter hash size: 517949
1328s Processed 513835 non-zero abundance kmers in kcounter.
1328s -Not sorting list of kmers, given parallel mode in effect.
1328s -beginning inchworm contig assembly.
1328s Total kcounter hash size: 517949 vs. sorted list size: 513835
1328s num threads set to: 2
1328s Done opening file. tmp.iworm.fa.pid_84445.thread_0
1328s Done opening file. tmp.iworm.fa.pid_84445.thread_1
1328s 
1328s 	Iworm contig assembly time: 0 seconds = 0 minutes.
1328s 
1329s TIMING CONTIG_BUILDING 0 s.
1329s 
1329s TIMING PROG_RUNTIME 1 s.
1329s * [Fri Nov  1 10:30:44 2024] Running CMD: mv /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa.tmp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa
1329s Friday, November 1, 2024: 10:30:44	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa.finished
1329s 
1329s 
1329s 
1329s #########################################################################
1329s Inchworm is complete.  --no_run_chrysalis was specified, so stopping here.
1329s #########################################################################
1329s 
1329s 
1329s 
1329s # stop before phase 2
1329s ${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
1329s 
1329s 
1329s      ______  ____   ____  ____   ____  ______  __ __
1329s     |      ||    \ |    ||    \ |    ||      ||  |  |
1329s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1329s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1329s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1329s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1329s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1329s 
1329s     Trinity-v2.15.1
1329s 
1329s 
1329s 
1329s Left read files: $VAR1 = [
1329s           'reads.left.fq.gz'
1329s         ];
1329s Right read files: $VAR1 = [
1329s           'reads.right.fq.gz'
1329s         ];
1329s 
1329s 
1329s ----------------------------------------------------------------------------------
1329s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1329s ----------------------------------------------------------------------------------
1329s 
1329s ---------------------------------------------------------------
1329s ------------ In silico Read Normalization ---------------------
1329s -- (Removing Excess Reads Beyond 200 Coverage --
1329s ---------------------------------------------------------------
1329s 
1329s # running normalization on reads: $VAR1 = [
1329s           [
1329s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
1329s           ],
1329s           [
1329s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
1329s           ]
1329s         ];
1329s 
1329s 
1329s --------------------------------------------------------
1329s -------------------- Chrysalis -------------------------
1329s -- (Contig Clustering & de Bruijn Graph Construction) --
1329s --------------------------------------------------------
1329s 
1329s inchworm_target: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1329s bowtie_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1329s chrysalis_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1329s 
1329s 
1329s #######################################################################
1329s Inchworm file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa detected.
1329s Skipping Inchworm Step, Using Previous Inchworm Assembly
1329s #######################################################################
1329s 
1329s * [Fri Nov  1 10:30:44 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa 100 10 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100
1329s * [Fri Nov  1 10:30:44 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 1>/dev/null
1329s * [Fri Nov  1 10:30:44 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam" 
1332s * [Fri Nov  1 10:30:47 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt
1333s * [Fri Nov  1 10:30:48 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt
1334s * [Fri Nov  1 10:30:49 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted
1334s * [Fri Nov  1 10:30:49 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1334s * [Fri Nov  1 10:30:49 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100  -weld_graph /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out
1334s * [Fri Nov  1 10:30:49 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -min 200
1334s * [Fri Nov  1 10:30:49 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa -f /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -p 10 
1338s * [Fri Nov  1 10:30:53 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.sort
1339s Friday, November 1, 2024: 10:30:54	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/read_partitions/Fb_0/CBin_0
1339s Friday, November 1, 2024: 10:30:54	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/partitioned_reads.files.list.ok
1339s Friday, November 1, 2024: 10:30:54	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.xkSdGF/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
1339s Friday, November 1, 2024: 10:30:54	CMD: touch recursive_trinity.cmds.ok
1339s Friday, November 1, 2024: 10:30:54	CMD: touch recursive_trinity.cmds.ok
1339s 
1339s 
1339s ###################################################################
1339s ##  Stopping here due to --no_distributed_trinity_exec in effect ##
1339s ###################################################################
1339s 
1339s 
1339s # finish it up
1339s ${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz  --CPU ${CPU} --output trinity_piecemeal 
1339s 
1339s 
1339s      ______  ____   ____  ____   ____  ______  __ __
1339s     |      ||    \ |    ||    \ |    ||      ||  |  |
1339s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1339s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1339s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1339s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1339s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1339s 
1339s     Trinity-v2.15.1
1339s 
1339s 
1339s 
1339s Left read files: $VAR1 = [
1339s           'reads.left.fq.gz'
1339s         ];
1339s Right read files: $VAR1 = [
1339s           'reads.right.fq.gz'
1339s         ];
1339s 
1339s 
1339s ----------------------------------------------------------------------------------
1339s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1339s ----------------------------------------------------------------------------------
1339s 
1339s ---------------------------------------------------------------
1339s ------------ In silico Read Normalization ---------------------
1339s -- (Removing Excess Reads Beyond 200 Coverage --
1339s ---------------------------------------------------------------
1339s 
1339s # running normalization on reads: $VAR1 = [
1339s           [
1339s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz'
1339s           ],
1339s           [
1339s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz'
1339s           ]
1339s         ];
1339s 
1339s 
1339s --------------------------------------------------------
1339s -------------------- Chrysalis -------------------------
1339s -- (Contig Clustering & de Bruijn Graph Construction) --
1339s --------------------------------------------------------
1339s 
1339s inchworm_target: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1339s bowtie_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1339s chrysalis_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa
1339s 
1339s 
1339s #######################################################################
1339s Inchworm file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa detected.
1339s Skipping Inchworm Step, Using Previous Inchworm Assembly
1339s #######################################################################
1339s 
1339s -- Skipping CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/inchworm.DS.fa 100 10 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100, checkpoint [/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100.ok] exists.
1339s -- Skipping CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 1>/dev/null, checkpoint [/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100.bowtie2-build.ok] exists.
1339s -- 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam" , checkpoint [/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam.ok] exists.
1339s -- Skipping CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt, checkpoint [/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt.ok] exists.
1339s -- Skipping CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt, checkpoint [/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.ok] exists.
1339s -- Skipping CMD: /usr/bin/sort --parallel=2 -T . -S 2G  -k9,9gr /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted, checkpoint [/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.ok] exists.
1339s -- Skipping CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames, checkpoint [/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames.ok] exists.
1339s -- Skipping CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/inchworm.DS.fa.min100  -weld_graph /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out, checkpoint [/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out.ok] exists.
1339s -- Skipping CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -min 200, checkpoint [/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta.ok] exists.
1339s -- Skipping CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa -f /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out -t 2 -max_mem_reads 50000000  -p 10 , checkpoint [/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.ok] exists.
1339s -- Skipping CMD: /usr/bin/sort --parallel=2 -T . -S 2G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.sort, checkpoint [/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/chrysalis/readsToComponents.out.sort.ok] exists.
1339s 
1339s 
1339s --------------------------------------------------------------------------------
1339s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1339s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1339s --------------------------------------------------------------------------------
1339s 
1339s Friday, November 1, 2024: 10:30:54	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
1339s Number of Commands: 38
1406s 
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.    
1406s 
1406s All commands completed successfully. :-)
1406s 
1406s 
1406s 
1406s ** Harvesting all assembled transcripts into a single multi-fasta file...
1406s 
1406s Friday, November 1, 2024: 10:32:01	CMD: find /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/Trinity.tmp
1406s * [Fri Nov  1 10:32:01 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa 2
1407s * [Fri Nov  1 10:32:02 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal/both.fa salmon_outdir/quant.sf 2 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta
1407s Friday, November 1, 2024: 10:32:02	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta.gene_trans_map
1407s 
1407s 
1407s #############################################################################
1407s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_piecemeal.Trinity.fasta
1407s #############################################################################
1407s 
1407s 
1407s ./misc_run_tests/__run_PE_samples_file.min_kmer_cov_3.sh
1407s 
1407s 
1407s 
1407s 
1407s ##### Done Running Trinity #####
1407s 
1407s exit 0
1407s #!/bin/bash -ve
1407s 
1407s ${TRINITY_HOME}/Trinity --samples_file samples.PE.txt \
1407s               --seqType fq \
1407s               --max_memory 1G \
1407s               --min_kmer_cov 3 \
1407s               --output trinity_test_samples_PE_min_kmer_cov_3
1407s 
1407s 
1407s      ______  ____   ____  ____   ____  ______  __ __
1407s     |      ||    \ |    ||    \ |    ||      ||  |  |
1407s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1407s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1407s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1407s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1407s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1407s 
1407s     Trinity-v2.15.1
1407s 
1407s 
1407s 
1407s Left read files: $VAR1 = [
1407s           'reads.left.fq.gz',
1407s           'reads2.left.fq.gz'
1407s         ];
1407s Right read files: $VAR1 = [
1407s           'reads.right.fq.gz',
1407s           'reads2.right.fq.gz'
1407s         ];
1407s Friday, November 1, 2024: 10:32:02	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3
1407s Friday, November 1, 2024: 10:32:02	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis
1407s 
1407s 
1407s ----------------------------------------------------------------------------------
1407s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1407s ----------------------------------------------------------------------------------
1407s 
1407s ---------------------------------------------------------------
1407s ------------ In silico Read Normalization ---------------------
1407s -- (Removing Excess Reads Beyond 200 Coverage --
1407s ---------------------------------------------------------------
1407s 
1407s # running normalization on reads: $VAR1 = [
1407s           [
1407s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz',
1407s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz'
1407s           ],
1407s           [
1407s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz',
1407s             '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz'
1407s           ]
1407s         ];
1407s 
1407s 
1407s Friday, November 1, 2024: 10:32:02	CMD: /usr/lib/trinityrnaseq/util/insilico_read_normalization.pl --seqType fq --JM 1G  --max_cov 200 --min_cov 3 --CPU 2 --output /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz --right /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz,/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz --pairs_together  --PARALLEL_STATS  
1407s -prepping seqs
1407s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz) >> left.fa
1407s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz) >> right.fa
1407s CMD finished (0 seconds)
1407s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz) >> left.fa
1407s CMD finished (0 seconds)
1407s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz) >> right.fa
1407s CMD finished (0 seconds)
1407s CMD finished (0 seconds)
1407s CMD: touch left.fa.ok
1407s CMD finished (0 seconds)
1407s CMD: touch right.fa.ok
1407s CMD finished (0 seconds)
1407s Done converting input files.CMD: cat left.fa right.fa > both.fa
1407s CMD finished (0 seconds)
1407s CMD: touch both.fa.ok
1407s CMD finished (0 seconds)
1407s -kmer counting.
1407s -------------------------------------------
1407s ----------- Jellyfish  --------------------
1407s -- (building a k-mer catalog from reads) --
1407s -------------------------------------------
1407s 
1407s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  both.fa
1409s CMD finished (2 seconds)
1409s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
1409s CMD finished (0 seconds)
1409s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
1409s CMD finished (0 seconds)
1409s CMD: touch jellyfish.K25.min2.kmers.fa.success
1409s CMD finished (0 seconds)
1409s -generating stats files
1409s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > left.fa.K25.stats
1409s -reading Kmer occurrences...
1409s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 1  --DS  > right.fa.K25.stats
1409s -reading Kmer occurrences...
1410s 
1410s  done parsing 518514 Kmers, 518514 added, taking 1 seconds.
1410s 
1410s  done parsing 518514 Kmers, 518514 added, taking 1 seconds.
1411s STATS_GENERATION_TIME: 1 seconds.
1411s STATS_GENERATION_TIME: 1 seconds.
1411s CMD finished (2 seconds)
1411s CMD finished (2 seconds)
1411s CMD: touch left.fa.K25.stats.ok
1411s CMD finished (0 seconds)
1411s CMD: touch right.fa.K25.stats.ok
1411s CMD finished (0 seconds)
1411s -sorting each stats file by read name.
1411s 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
1411s 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
1411s CMD finished (0 seconds)
1411s CMD finished (0 seconds)
1411s CMD: touch left.fa.K25.stats.sort.ok
1411s CMD finished (0 seconds)
1411s CMD: touch right.fa.K25.stats.sort.ok
1411s CMD finished (0 seconds)
1411s -defining normalized reads
1411s 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
1411s -opening left.fa.K25.stats.sort
1411s -opening right.fa.K25.stats.sort
1411s -done opening files.
1412s CMD finished (1 seconds)
1412s CMD: touch pairs.K25.stats.ok
1412s CMD finished (0 seconds)
1412s 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
1413s 53574 / 61150 = 87.61% reads selected during normalization.
1413s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles.
1413s 2974 / 61150 = 4.86% reads discarded as below minimum coverage threshold=3
1413s CMD finished (1 seconds)
1413s CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
1413s CMD finished (0 seconds)
1413s -search and capture.
1413s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz ... done prepping, now search and capture.
1413s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz
1413s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz ... done prepping, now search and capture.
1413s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
1413s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz
1413s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz
1414s CMD: touch /tmp/autopkgtest.xkSdGF/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
1414s CMD finished (0 seconds)
1414s CMD: touch /tmp/autopkgtest.xkSdGF/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
1414s CMD finished (0 seconds)
1414s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
1414s CMD finished (0 seconds)
1414s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
1414s CMD finished (0 seconds)
1414s -removing tmp dir /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/tmp_normalized_reads
1414s 
1414s 
1414s Normalization complete. See outputs: 
1414s 	/tmp/autopkgtest.xkSdGF/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
1414s 	/tmp/autopkgtest.xkSdGF/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
1414s Friday, November 1, 2024: 10:32:09	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/insilico_read_normalization/normalization.ok
1414s Converting input files. (in parallel)Friday, November 1, 2024: 10:32:09	CMD: cat /tmp/autopkgtest.xkSdGF/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
1414s Friday, November 1, 2024: 10:32:09	CMD: cat /tmp/autopkgtest.xkSdGF/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
1414s Friday, November 1, 2024: 10:32:09	CMD: touch left.fa.ok
1414s Friday, November 1, 2024: 10:32:09	CMD: touch right.fa.ok
1414s Friday, November 1, 2024: 10:32:09	CMD: touch left.fa.ok right.fa.ok
1414s Friday, November 1, 2024: 10:32:09	CMD: cat left.fa right.fa > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
1414s Friday, November 1, 2024: 10:32:09	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa.ok
1414s -------------------------------------------
1414s ----------- Jellyfish  --------------------
1414s -- (building a k-mer (25) catalog from reads) --
1414s -------------------------------------------
1414s 
1414s * [Fri Nov  1 10:32:09 2024] Running CMD: jellyfish count -t 2 -m 25 -s 100000000 -o mer_counts.25.asm.jf --canonical  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
1416s * [Fri Nov  1 10:32:11 2024] Running CMD: jellyfish dump -L 3 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
1416s * [Fri Nov  1 10:32:11 2024] Running CMD: jellyfish histo -t 2 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
1416s ----------------------------------------------
1416s --------------- Inchworm (K=25, asm) ---------------------
1416s -- (Linear contig construction from k-mers) --
1416s ----------------------------------------------
1416s 
1416s * [Fri Nov  1 10:32:11 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa.tmp
1416s Kmer length set to: 25
1416s Min assembly length set to: 25
1416s Monitor turned on, set to: 1
1416s double stranded mode set
1416s min entropy set to: 1
1416s setting number of threads to: 2
1416s -setting parallel iworm mode.
1416s -reading Kmer occurrences...
1416s 
1416s  done parsing 96295 Kmers, 96295 added, taking 0 seconds.
1416s 
1416s TIMING KMER_DB_BUILDING 0 s.
1416s Pruning kmers (min_kmer_count=1 min_any_entropy=1 min_ratio_non_error=0.005)
1416s Pruned 474 kmers from catalog.
1416s 	Pruning time: 0 seconds = 0 minutes.
1416s 
1416s TIMING PRUNING 0 s.
1416s -populating the kmer seed candidate list.
1416s Kcounter hash size: 96295
1416s Processed 95821 non-zero abundance kmers in kcounter.
1416s -Not sorting list of kmers, given parallel mode in effect.
1416s -beginning inchworm contig assembly.
1416s Total kcounter hash size: 96295 vs. sorted list size: 95821
1416s num threads set to: 2
1416s Done opening file. tmp.iworm.fa.pid_91322.thread_0
1416s Done opening file. tmp.iworm.fa.pid_91322.thread_1
1416s 
1416s 	Iworm contig assembly time: 0 seconds = 0 minutes.
1416s 
1416s TIMING CONTIG_BUILDING 0 s.
1416s 
1416s TIMING PROG_RUNTIME 0 s.
1416s * [Fri Nov  1 10:32:11 2024] Running CMD: mv /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa.tmp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa
1416s Friday, November 1, 2024: 10:32:11	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa.finished
1416s --------------------------------------------------------
1416s -------------------- Chrysalis -------------------------
1416s -- (Contig Clustering & de Bruijn Graph Construction) --
1416s --------------------------------------------------------
1416s 
1416s inchworm_target: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
1416s bowtie_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
1416s chrysalis_reads_fa: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa
1416s * [Fri Nov  1 10:32:11 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/inchworm.DS.fa 100 10 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100
1416s * [Fri Nov  1 10:32:11 2024] Running CMD: /usr/bin/bowtie2-build --threads 2 -o 3 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 1>/dev/null
1417s * [Fri Nov  1 10:32:12 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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm.bowtie.nameSorted.bam" 
1421s * [Fri Nov  1 10:32:16 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm.bowtie.nameSorted.bam /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_scaffolds.txt
1422s * [Fri Nov  1 10:32:17 2024] Running CMD: /usr/bin/GraphFromFasta -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 -r /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_scaffolds.txt  > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt
1425s * [Fri Nov  1 10:32:20 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G  -k9,9gr /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt.sorted
1425s * [Fri Nov  1 10:32:20 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/inchworm.DS.fa.min100 /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
1425s * [Fri Nov  1 10:32:20 2024] Running CMD: /usr/bin/BubbleUpClustering -i /tmp/autopkgtest.xkSdGF/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.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/GraphFromIwormFasta.out
1425s * [Fri Nov  1 10:32:20 2024] Running CMD: /usr/bin/CreateIwormFastaBundle -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/GraphFromIwormFasta.out -o /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/bundled_iworm_contigs.fasta -min 200
1425s * [Fri Nov  1 10:32:20 2024] Running CMD: /usr/bin/ReadsToTranscripts -i /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa -f /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/bundled_iworm_contigs.fasta -o /tmp/autopkgtest.xkSdGF/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 
1432s * [Fri Nov  1 10:32:27 2024] Running CMD: /usr/bin/sort --parallel=2 -T . -S 1G -k 1,1n -k3,3nr -k2,2 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/readsToComponents.out > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/chrysalis/readsToComponents.out.sort
1432s Friday, November 1, 2024: 10:32:27	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/read_partitions/Fb_0/CBin_0
1432s Friday, November 1, 2024: 10:32:27	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/partitioned_reads.files.list.ok
1432s Friday, November 1, 2024: 10:32:27	CMD: /usr/lib/trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /tmp/autopkgtest.xkSdGF/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
1432s Friday, November 1, 2024: 10:32:27	CMD: touch recursive_trinity.cmds.ok
1432s Friday, November 1, 2024: 10:32:27	CMD: touch recursive_trinity.cmds.ok
1432s 
1432s 
1432s --------------------------------------------------------------------------------
1432s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1432s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1432s --------------------------------------------------------------------------------
1432s 
1432s Friday, November 1, 2024: 10:32:27	CMD: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle 
1432s Number of Commands: 17
1493s 
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.    
1493s 
1493s All commands completed successfully. :-)
1493s 
1493s 
1493s 
1493s ** Harvesting all assembled transcripts into a single multi-fasta file...
1493s 
1493s Friday, November 1, 2024: 10:33:28	CMD: find /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/Trinity.tmp
1494s * [Fri Nov  1 10:33:28 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3/both.fa 2
1494s * [Fri Nov  1 10:33:29 2024] Running CMD: /usr/lib/trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta
1494s Friday, November 1, 2024: 10:33:29	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta.gene_trans_map
1494s 
1494s 
1494s #############################################################################
1494s Finished.  Final Trinity assemblies are written to /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly/trinity_test_samples_PE_min_kmer_cov_3.Trinity.fasta
1494s #############################################################################
1494s 
1494s 
1495s touch test_all
1495s make[1]: Leaving directory '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly'
1495s 
1495s 
1495s exit 0
1495s Running example in test_GenomeGuidedTrinity...
1495s make[1]: Entering directory '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity'
1495s ./run_genome-guided_Trinity_use_existing_bam.sh
1495s #!/bin/bash -ve
1495s 
1495s if [ -e top100k.Left.fq.gz ] && ! [ -e top100k.Left.fq ]
1495s then
1495s 	gunzip -c top100k.Left.fq.gz > top100k.Left.fq
1495s fi
1495s 
1495s if [ -e top100k.Right.fq.gz ] && ! [ -e top100k.Right.fq ]
1495s then
1495s 	gunzip -c top100k.Right.fq.gz > top100k.Right.fq
1495s fi
1495s 
1495s 
1495s 
1495s if [ -e top100k.genome.gz ] && ! [ -e top100k.genome ]
1495s then
1495s 	gunzip -c top100k.genome.gz > top100k.genome
1495s fi
1495s 
1495s 
1495s 
1495s $TRINITY_HOME/Trinity --genome_guided_max_intron 1000 --genome_guided_bam SP2.chr.bam --max_memory 2G  --output test_GG_use_bam_trinity_outdir
1495s 
1495s 
1495s      ______  ____   ____  ____   ____  ______  __ __
1495s     |      ||    \ |    ||    \ |    ||      ||  |  |
1495s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1495s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1495s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1495s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1495s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1495s 
1495s     Trinity-v2.15.1
1495s 
1495s 
1495s 
1495s Friday, November 1, 2024: 10:33:30	CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl SP2.chr.bam
1495s -appears to be a coordinate sorted bam file. ok.
1495s Friday, November 1, 2024: 10:33:30	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir
1495s 
1495s 
1495s ----------------------------------------------------------------------------------
1495s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1495s ----------------------------------------------------------------------------------
1495s 
1495s -found paired-end aligned read. Running in paired-end mode.
1495s Friday, November 1, 2024: 10:33:30	CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/SP2.chr.bam
1496s Friday, November 1, 2024: 10:33:31	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/SP2.chr.bam.norm_200.bam.ok
1496s Friday, November 1, 2024: 10:33:31	CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.xkSdGF/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 
1496s 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 
1496s -extracting read coordinates from SP2.chr.bam.norm_200.bam into SP2.chr.bam.norm_200.bam.read_coords
1496s 
1497s CMD: touch SP2.chr.bam.norm_200.bam.read_coords.ok
1497s 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
1497s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
1497s 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
1497s 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
1498s 
[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
1498s 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
1498s CMD: touch SP2.chr.bam.norm_200.bam.minC1.gff.ok
1498s 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 
1498s // parsing paritions.
1498s 
[71]  -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/14_122.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/212_1291.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/1392_1648.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/1797_2125.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/2163_3611.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/3633_3710.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/4913_5681.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/9938_10435.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/11319_11903.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/12073_12996.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/13623_13950.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/14321_14565.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/15124_16713.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/16949_17135.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17151_17239.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17291_17395.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17403_17460.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/17486_18615.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/18669_19255.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/19312_19749.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/19806_20057.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/25542_25904.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/27107_27961.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/29764_32484.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/33570_35223.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/35276_35333.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/35616_35657.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/35667_36204.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/40913_41816.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/42003_43278.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/43414_43636.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/45059_45550.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/45591_49924.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/50916_53857.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/54299_54404.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/56263_56322.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/56460_59191.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/59428_61023.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/64539_69762.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/71026_71306.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/71566_71786.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/72348_72436.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/73883_73950.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/76379_76542.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/77783_78299.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/79543_79626.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/80570_80778.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/81974_82231.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/85575_85999.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/90691_93939.trinity.reads
1498s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/95200_96973.trinity.reads
1499s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/98644_98711.trinity.reads
1499s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads
1499s -writing to Dir_SP2.chr.bam.norm_200.bam.minC1.gff/7000000090838467/0/99132_100027.trinity.reads
1499s CMD: touch Dir_SP2.chr.bam.norm_200.bam.minC1.gff.ok
1499s ##
1499s Done
1499s ##
1499s 
1499s Friday, November 1, 2024: 10:33:33	CMD: touch partitions.ok
1499s Friday, November 1, 2024: 10:33:33	CMD: find Dir_* -name '*reads' > read_files.list
1499s Friday, November 1, 2024: 10:33:34	CMD: touch read_files.list.ok
1499s Friday, November 1, 2024: 10:33:34	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
1499s Friday, November 1, 2024: 10:33:34	CMD: touch trinity_GG.cmds.ok
1499s Friday, November 1, 2024: 10:33:34	CMD: touch trinity_GG.cmds.ok
1499s 
1499s 
1499s --------------------------------------------------------------------------------
1499s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1499s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1499s --------------------------------------------------------------------------------
1499s 
1499s Friday, November 1, 2024: 10:33:34	CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -v -shuffle 
1499s Number of Commands: 37
1553s 
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.    
1553s 
1553s All commands completed successfully. :-)
1553s 
1553s Friday, November 1, 2024: 10:34:28	CMD: find Dir_*  -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta.tmp
1553s Friday, November 1, 2024: 10:34:28	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta.gene_trans_map
1553s 
1553s 
1553s Finished. See /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_bam_trinity_outdir/Trinity-GG.fasta for reconstructed transcripts
1553s 
1553s 
1553s asmsize=$(wc -c <"test_GG_use_bam_trinity_outdir/Trinity-GG.fasta")
1553s if [ $asmsize -le 50000 ]; then
1553s     echo "Error, test_GG_use_bam_trinity_outdir/Trinity-GG.fasta potentially incomplete"
1553s     exit 1
1553s else
1553s     echo "ok"
1553s     exit 0
1553s fi
1553s #!/bin/bash -ve
1553s 
1553s $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
1553s ok
1553s ./run_Schizo_TrinityGG_jaccard_clip.sh
1553s 
1553s 
1553s      ______  ____   ____  ____   ____  ______  __ __
1553s     |      ||    \ |    ||    \ |    ||      ||  |  |
1553s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1553s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1553s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1553s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1553s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1553s 
1553s     Trinity-v2.15.1
1553s 
1553s 
1553s 
1553s Friday, November 1, 2024: 10:34:28	CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl SP2.chr.bam
1554s -appears to be a coordinate sorted bam file. ok.
1554s Friday, November 1, 2024: 10:34:29	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir
1554s 
1554s 
1554s ----------------------------------------------------------------------------------
1554s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1554s ----------------------------------------------------------------------------------
1554s 
1554s -found paired-end aligned read. Running in paired-end mode.
1554s Friday, November 1, 2024: 10:34:29	CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/SP2.chr.bam
1554s Friday, November 1, 2024: 10:34:29	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam.ok
1554s Friday, November 1, 2024: 10:34:29	CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.xkSdGF/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 
1554s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/SP2.chr.bam.norm_200.bam RF
1555s 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 
1555s 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 
1555s -extracting read coordinates from SP2.chr.bam.norm_200.bam.+.sam into SP2.chr.bam.norm_200.bam.+.sam.read_coords
1555s 
1555s -extracting read coordinates from SP2.chr.bam.norm_200.bam.-.sam into SP2.chr.bam.norm_200.bam.-.sam.read_coords
1555s 
1555s CMD: touch SP2.chr.bam.norm_200.bam.-.sam.read_coords.ok
1555s 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
1555s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
1555s 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
1555s 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
1555s 
[1000 lines read]  scaff:7000000090838467 lend:6194  rend:6433     CMD: touch SP2.chr.bam.norm_200.bam.+.sam.read_coords.ok
1555s 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
1555s 
[2000 lines read]  scaff:7000000090838467 lend:46308  rend:46696     
[3000 lines read]  scaff:7000000090838467 lend:59573  rend:59951     
[4000 lines read]  scaff:7000000090838467 lend:60068  rend:60313     CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
1555s 
[5000 lines read]  scaff:7000000090838467 lend:60602  rend:60807     
[6000 lines read]  scaff:7000000090838467 lend:65099  rend:65468     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
1555s 
[7000 lines read]  scaff:7000000090838467 lend:65621  rend:65957     
[8000 lines read]  scaff:7000000090838467 lend:66173  rend:66538     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
1555s 
[9000 lines read]  scaff:7000000090838467 lend:88962  rend:89278     
[1000 lines read]  scaff:7000000090838467 lend:8022  rend:8237     CMD: touch SP2.chr.bam.norm_200.bam.-.sam.frag_coverage.wig.ok
1555s 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
1556s 
[2000 lines read]  scaff:7000000090838467 lend:8568  rend:8635     
[3000 lines read]  scaff:7000000090838467 lend:21591  rend:21888     
[4000 lines read]  scaff:7000000090838467 lend:29215  rend:29340     
[5000 lines read]  scaff:7000000090838467 lend:30519  rend:30759     
[6000 lines read]  scaff:7000000090838467 lend:52660  rend:52989     
[7000 lines read]  scaff:7000000090838467 lend:56475  rend:56834     CMD: touch SP2.chr.bam.norm_200.bam.-.sam.minC1.gff.ok
1556s 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 
1556s 
[8000 lines read]  scaff:7000000090838467 lend:57224  rend:57489     // parsing paritions.
1556s 
[73]  -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/14_122.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/212_1291.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/1392_1648.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/1797_2125.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/2163_3469.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3633_3710.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/3755_4851.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/4913_5470.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5606_5681.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/5739_6633.trinity.reads
1556s 
[9000 lines read]  scaff:7000000090838467 lend:67627  rend:67818     
[10000 lines read]  scaff:7000000090838467 lend:68505  rend:68690     -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/7478_7778.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/11319_11575.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/12073_12957.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/13623_13950.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15124_15496.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/15840_16130.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/16160_16227.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/16322_16713.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/16949_17135.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/17955_18310.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/18334_18615.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/18745_19255.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/19312_19749.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/19806_20057.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/21538_21869.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/25632_25904.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/27297_27961.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/28689_28755.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/28953_29020.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/31012_32484.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/33570_34392.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/35276_35333.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/35667_36050.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/40961_41816.trinity.reads
1556s 
[11000 lines read]  scaff:7000000090838467 lend:69245  rend:69544     -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/42003_42940.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/43050_43256.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/43414_43636.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/45591_48387.trinity.reads
1556s 
[12000 lines read]  scaff:7000000090838467 lend:82862  rend:83065     -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/50916_51540.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/52320_52590.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/52965_53480.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/54299_54404.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55029_55235.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55243_55272.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55367_55660.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/55765_56138.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56263_56322.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/56463_57542.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/57818_59191.trinity.reads
1556s 
[13000 lines read]  scaff:7000000090838467 lend:83622  rend:83842     -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/59428_61000.trinity.reads
1556s 
[14000 lines read]  scaff:7000000090838467 lend:84137  rend:84436     CMD: touch SP2.chr.bam.norm_200.bam.+.sam.frag_coverage.wig.ok
1556s 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
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/63225_63476.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/64539_67074.trinity.reads
1556s CMD: touch SP2.chr.bam.norm_200.bam.+.sam.minC1.gff.ok
1556s 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 
1556s // parsing paritions.
1556s 
[57]  -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/872_939.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/963_1208.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/2378_2430.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/3465_3611.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/3804_3872.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/5374_5664.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/7449_9363.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/67085_67370.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/69270_69337.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/71566_71786.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/73883_73950.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/74480_76014.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/76379_76542.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/77783_78299.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80570_80778.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/80871_81360.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81545_81938.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/81974_82231.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/83425_83673.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/83688_83987.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/84011_84078.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/85575_85999.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/88224_90282.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/90691_92023.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/92400_93867.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/95200_96782.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/98744_98781.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff/7000000090838467/0/99132_99997.trinity.reads
1556s CMD: touch Dir_SP2.chr.bam.norm_200.bam.-.sam.minC1.gff.ok
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/9938_10435.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/11471_11903.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/12115_12996.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/14321_14565.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/15279_16382.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/17151_18545.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/18669_18911.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/20899_21018.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/21381_22953.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/25542_25867.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/27107_27395.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/27630_27959.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/28532_29661.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/29764_31480.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/31628_31881.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/31893_32259.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/32495_33171.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/33742_35223.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/35616_35657.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/35987_36204.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/39223_40535.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/40913_41123.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/41133_41404.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/42029_43278.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/45059_45550.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/46429_46482.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/47355_49924.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/50261_50810.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/51096_53857.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/54954_56228.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/56460_58094.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/58444_58978.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/59886_59966.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/60255_61023.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/62962_63858.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/64782_64821.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/65880_65925.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/66238_69762.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/71026_71306.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/72348_72436.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/76741_77546.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/79543_79626.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/82248_84785.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/88618_88826.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/91010_93939.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/95801_96973.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98644_98711.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/98739_98839.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99067_99099.trinity.reads
1556s -writing to Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff/7000000090838467/0/99339_100027.trinity.reads
1556s CMD: touch Dir_SP2.chr.bam.norm_200.bam.+.sam.minC1.gff.ok
1556s ##
1556s Done
1556s ##
1556s 
1556s Friday, November 1, 2024: 10:34:31	CMD: touch partitions.ok
1556s Friday, November 1, 2024: 10:34:31	CMD: find Dir_* -name '*reads' > read_files.list
1556s Friday, November 1, 2024: 10:34:31	CMD: touch read_files.list.ok
1556s Friday, November 1, 2024: 10:34:31	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
1556s Friday, November 1, 2024: 10:34:31	CMD: touch trinity_GG.cmds.ok
1556s Friday, November 1, 2024: 10:34:31	CMD: touch trinity_GG.cmds.ok
1556s 
1556s 
1556s --------------------------------------------------------------------------------
1556s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1556s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1556s --------------------------------------------------------------------------------
1556s 
1556s Friday, November 1, 2024: 10:34:31	CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -v -shuffle 
1556s Number of Commands: 53
1557s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1557s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1557s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s bt2 index files: $VAR1 = [];
1557s Note - bowtie-build indices do not yet exist. Indexing genome now.
1557s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s bt2 index files: $VAR1 = [];
1557s Note - bowtie-build indices do not yet exist. Indexing genome now.
1557s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1557s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1557s 10 reads; of these:
1557s   10 (100.00%) were unpaired; of these:
1557s     3 (30.00%) aligned 0 times
1557s     7 (70.00%) aligned exactly 1 time
1557s     0 (0.00%) aligned >1 times
1557s 70.00% overall alignment rate
1557s 76 reads; of these:
1557s   76 (100.00%) were unpaired; of these:
1557s     0 (0.00%) aligned 0 times
1557s     76 (100.00%) aligned exactly 1 time
1557s     0 (0.00%) aligned >1 times
1557s 100.00% overall alignment rate
1557s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s 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
1557s 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
1557s 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 
1557s 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 
1557s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1557s 
1557s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1557s 
1557s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1557s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1557s 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
1557s 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
1557s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s 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
1557s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s 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
1557s 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 
1557s 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 
1557s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1557s -processing jaccard pair sensor
1557s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1557s 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
1557s -processing jaccard pair sensor
1557s 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
1557s 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
1557s 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
1557s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1557s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1558s 
succeeded(1)   1.88679% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1558s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1558s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1558s bt2 index files: $VAR1 = [];
1558s Note - bowtie-build indices do not yet exist. Indexing genome now.
1558s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1558s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1558s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1558s 24 reads; of these:
1558s   24 (100.00%) were unpaired; of these:
1558s     1 (4.17%) aligned 0 times
1558s     23 (95.83%) aligned exactly 1 time
1558s     0 (0.00%) aligned >1 times
1558s 95.83% overall alignment rate
1558s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1558s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1558s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1558s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1558s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1558s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1558s 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
1558s 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 
1558s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1558s 
1558s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1558s 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
1558s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1558s 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
1558s 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 
1558s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1558s -processing jaccard pair sensor
1558s 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
1558s 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
1558s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1559s 
succeeded(2)   3.77358% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1559s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1559s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1559s bt2 index files: $VAR1 = [];
1559s Note - bowtie-build indices do not yet exist. Indexing genome now.
1559s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1559s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1559s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1560s 18 reads; of these:
1560s   18 (100.00%) were unpaired; of these:
1560s     1 (5.56%) aligned 0 times
1560s     17 (94.44%) aligned exactly 1 time
1560s     0 (0.00%) aligned >1 times
1560s 94.44% overall alignment rate
1560s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1560s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1560s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1560s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1560s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1560s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1560s 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
1560s 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 
1560s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1560s 
1560s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1560s 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
1560s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1560s 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
1560s 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 
1560s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1560s -processing jaccard pair sensor
1560s 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
1560s 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
1560s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1560s 
succeeded(3)   5.66038% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1560s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1561s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1561s bt2 index files: $VAR1 = [];
1561s Note - bowtie-build indices do not yet exist. Indexing genome now.
1561s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1561s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1561s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1561s 
succeeded(4)   7.54717% completed.    1811 reads; of these:
1561s   1811 (100.00%) were unpaired; of these:
1561s     6 (0.33%) aligned 0 times
1561s     1189 (65.65%) aligned exactly 1 time
1561s     616 (34.01%) aligned >1 times
1561s 99.67% overall alignment rate
1561s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1561s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1561s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1561s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1561s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1561s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1561s 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
1561s 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 
1561s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1561s 
1561s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1561s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1561s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1561s 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
1561s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1561s 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
1561s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1561s 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 
1561s bt2 index files: $VAR1 = [];
1561s Note - bowtie-build indices do not yet exist. Indexing genome now.
1561s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1561s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1561s -processing jaccard pair sensor
1561s 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
1561s 
[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
1561s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1561s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1561s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1562s 818 reads; of these:
1562s   818 (100.00%) were unpaired; of these:
1562s     1 (0.12%) aligned 0 times
1562s     758 (92.67%) aligned exactly 1 time
1562s     59 (7.21%) aligned >1 times
1562s 99.88% overall alignment rate
1562s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1562s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1562s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1562s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1562s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1562s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1562s 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
1562s 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 
1562s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1562s 
1562s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1562s 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
1562s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1562s 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
1562s 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 
1562s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1562s -processing jaccard pair sensor
1562s 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
1562s 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
1562s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1565s 
succeeded(5)   9.43396% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1565s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1565s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1565s bt2 index files: $VAR1 = [];
1565s Note - bowtie-build indices do not yet exist. Indexing genome now.
1565s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1565s 
succeeded(6)   11.3208% completed.    CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1565s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1565s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1565s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1565s 30 reads; of these:
1565s   30 (100.00%) were unpaired; of these:
1565s     0 (0.00%) aligned 0 times
1565s     18 (60.00%) aligned exactly 1 time
1565s     12 (40.00%) aligned >1 times
1565s 100.00% overall alignment rate
1565s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1565s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1565s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1565s bt2 index files: $VAR1 = [];
1565s Note - bowtie-build indices do not yet exist. Indexing genome now.
1565s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1565s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1565s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1565s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1565s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1565s 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
1565s 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 
1565s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1565s 
1565s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1565s 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
1565s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1565s 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
1565s 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 
1565s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1565s -processing jaccard pair sensor
1565s 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
1565s 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
1565s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1565s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1565s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1566s 85 reads; of these:
1566s   85 (100.00%) were unpaired; of these:
1566s     6 (7.06%) aligned 0 times
1566s     79 (92.94%) aligned exactly 1 time
1566s     0 (0.00%) aligned >1 times
1566s 92.94% overall alignment rate
1566s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1566s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1566s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1566s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1566s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1566s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1566s 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
1566s 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 
1566s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1566s 
1566s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1566s 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
1566s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1566s 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
1566s 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 
1566s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1566s -processing jaccard pair sensor
1566s 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
1566s 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
1566s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1566s 
succeeded(7)   13.2075% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1566s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1566s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1566s bt2 index files: $VAR1 = [];
1566s Note - bowtie-build indices do not yet exist. Indexing genome now.
1566s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1567s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1567s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1567s 10 reads; of these:
1567s   10 (100.00%) were unpaired; of these:
1567s     7 (70.00%) aligned 0 times
1567s     3 (30.00%) aligned exactly 1 time
1567s     0 (0.00%) aligned >1 times
1567s 30.00% overall alignment rate
1567s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1567s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1567s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1567s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1567s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1567s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1567s 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
1567s 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 
1567s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1567s 
1567s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1567s 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
1567s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1567s 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
1567s 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 
1567s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1567s -processing jaccard pair sensor
1567s 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
1567s 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
1567s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s 
succeeded(8)   15.0943% completed.    
succeeded(9)   16.9811% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1568s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s bt2 index files: $VAR1 = [];
1568s Note - bowtie-build indices do not yet exist. Indexing genome now.
1568s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1568s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s bt2 index files: $VAR1 = [];
1568s Note - bowtie-build indices do not yet exist. Indexing genome now.
1568s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1568s 98 reads; of these:
1568s   98 (100.00%) were unpaired; of these:
1568s     0 (0.00%) aligned 0 times
1568s     98 (100.00%) aligned exactly 1 time
1568s     0 (0.00%) aligned >1 times
1568s 100.00% overall alignment rate
1568s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s 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
1568s 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 
1568s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1568s 
1568s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1568s 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
1568s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s 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
1568s 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 
1568s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1568s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1568s -processing jaccard pair sensor
1568s 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
1568s 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
1568s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s 145 reads; of these:
1568s   145 (100.00%) were unpaired; of these:
1568s     1 (0.69%) aligned 0 times
1568s     144 (99.31%) aligned exactly 1 time
1568s     0 (0.00%) aligned >1 times
1568s 99.31% overall alignment rate
1568s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1568s 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
1568s 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 
1569s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1569s 
1569s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1569s 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
1569s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1569s 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
1569s 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 
1569s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1569s -processing jaccard pair sensor
1569s 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
1569s 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
1569s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1571s 
succeeded(10)   18.8679% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1571s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1571s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1571s bt2 index files: $VAR1 = [];
1571s Note - bowtie-build indices do not yet exist. Indexing genome now.
1571s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1571s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1571s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1571s 26 reads; of these:
1571s   26 (100.00%) were unpaired; of these:
1571s     17 (65.38%) aligned 0 times
1571s     9 (34.62%) aligned exactly 1 time
1571s     0 (0.00%) aligned >1 times
1571s 34.62% overall alignment rate
1571s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1571s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1571s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1571s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1571s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1571s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1571s 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
1571s 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 
1571s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1571s 
1571s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1571s 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
1571s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1571s 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
1571s 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 
1571s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1571s -processing jaccard pair sensor
1571s 
succeeded(11)   20.7547% completed.    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
1571s 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
1571s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1571s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1571s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1571s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1571s bt2 index files: $VAR1 = [];
1571s Note - bowtie-build indices do not yet exist. Indexing genome now.
1571s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1572s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1572s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1572s 42 reads; of these:
1572s   42 (100.00%) were unpaired; of these:
1572s     18 (42.86%) aligned 0 times
1572s     24 (57.14%) aligned exactly 1 time
1572s     0 (0.00%) aligned >1 times
1572s 57.14% overall alignment rate
1572s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1572s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1572s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1572s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1572s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1572s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1572s 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
1572s 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 
1572s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1572s 
1572s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1572s 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
1572s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1572s 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
1572s 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 
1572s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1572s -processing jaccard pair sensor
1572s 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
1572s 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
1572s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1572s 
succeeded(12)   22.6415% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1572s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1572s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1572s bt2 index files: $VAR1 = [];
1572s Note - bowtie-build indices do not yet exist. Indexing genome now.
1572s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1572s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1572s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1573s 26 reads; of these:
1573s   26 (100.00%) were unpaired; of these:
1573s     6 (23.08%) aligned 0 times
1573s     20 (76.92%) aligned exactly 1 time
1573s     0 (0.00%) aligned >1 times
1573s 76.92% overall alignment rate
1573s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s 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
1573s 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 
1573s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1573s 
1573s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1573s 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
1573s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s 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
1573s 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 
1573s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1573s -processing jaccard pair sensor
1573s 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
1573s 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
1573s 
succeeded(13)   24.5283% completed.    CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1573s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s bt2 index files: $VAR1 = [];
1573s Note - bowtie-build indices do not yet exist. Indexing genome now.
1573s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1573s 293 reads; of these:
1573s   293 (100.00%) were unpaired; of these:
1573s     0 (0.00%) aligned 0 times
1573s     293 (100.00%) aligned exactly 1 time
1573s     0 (0.00%) aligned >1 times
1573s 100.00% overall alignment rate
1573s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s 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
1573s 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 
1573s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1573s 
1573s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1573s 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
1573s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1573s 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
1573s 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 
1573s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1573s -processing jaccard pair sensor
1573s 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
1574s 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
1574s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1575s 
succeeded(14)   26.4151% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1575s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1575s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1575s bt2 index files: $VAR1 = [];
1575s Note - bowtie-build indices do not yet exist. Indexing genome now.
1575s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1575s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1575s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1575s 309 reads; of these:
1575s   309 (100.00%) were unpaired; of these:
1575s     3 (0.97%) aligned 0 times
1575s     201 (65.05%) aligned exactly 1 time
1575s     105 (33.98%) aligned >1 times
1575s 99.03% overall alignment rate
1575s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1575s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1575s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1575s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1575s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1575s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1575s 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
1575s 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 
1575s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1575s 
1575s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1575s 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
1575s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1575s 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
1575s 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 
1575s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1575s -processing jaccard pair sensor
1575s 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
1575s 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
1576s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1576s 
succeeded(15)   28.3019% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1576s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1576s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1576s bt2 index files: $VAR1 = [];
1576s Note - bowtie-build indices do not yet exist. Indexing genome now.
1576s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1576s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1576s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1576s 27 reads; of these:
1576s   27 (100.00%) were unpaired; of these:
1576s     6 (22.22%) aligned 0 times
1576s     21 (77.78%) aligned exactly 1 time
1576s     0 (0.00%) aligned >1 times
1576s 77.78% overall alignment rate
1576s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1576s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1576s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1576s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1576s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1576s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1576s 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
1576s 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 
1576s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1576s 
1576s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1576s 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
1576s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1577s 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
1577s 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 
1577s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1577s -processing jaccard pair sensor
1577s 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
1577s 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
1577s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s 
succeeded(16)   30.1887% completed.    
succeeded(17)   32.0755% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1578s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1578s bt2 index files: $VAR1 = [];
1578s Note - bowtie-build indices do not yet exist. Indexing genome now.
1578s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s bt2 index files: $VAR1 = [];
1578s Note - bowtie-build indices do not yet exist. Indexing genome now.
1578s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1578s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1578s 24 reads; of these:
1578s   24 (100.00%) were unpaired; of these:
1578s     3 (12.50%) aligned 0 times
1578s     21 (87.50%) aligned exactly 1 time
1578s     0 (0.00%) aligned >1 times
1578s 87.50% overall alignment rate
1578s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s 953 reads; of these:
1578s   953 (100.00%) were unpaired; of these:
1578s     4 (0.42%) aligned 0 times
1578s     555 (58.24%) aligned exactly 1 time
1578s     394 (41.34%) aligned >1 times
1578s 99.58% overall alignment rate
1578s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s 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
1578s 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 
1578s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1578s 
1578s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1578s 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
1578s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s 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
1578s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1578s 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 
1578s 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
1578s 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 
1578s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1578s -processing jaccard pair sensor
1578s 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
1578s 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
1579s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1579s 
1579s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1579s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1579s 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
1579s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1579s 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
1579s 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 
1579s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1579s -processing jaccard pair sensor
1579s 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
1579s 
[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
1579s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1580s 
succeeded(18)   33.9623% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1580s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1580s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1580s bt2 index files: $VAR1 = [];
1580s Note - bowtie-build indices do not yet exist. Indexing genome now.
1580s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1580s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1580s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1581s 16 reads; of these:
1581s   16 (100.00%) were unpaired; of these:
1581s     10 (62.50%) aligned 0 times
1581s     6 (37.50%) aligned exactly 1 time
1581s     0 (0.00%) aligned >1 times
1581s 37.50% overall alignment rate
1581s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1581s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1581s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1581s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1581s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1581s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1581s 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
1581s 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 
1581s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1581s 
1581s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1581s 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
1581s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1581s 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
1581s 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 
1581s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1581s -processing jaccard pair sensor
1581s 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
1581s 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
1581s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1582s 
succeeded(19)   35.8491% completed.    
succeeded(20)   37.7359% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1582s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1582s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s bt2 index files: $VAR1 = [];
1583s Note - bowtie-build indices do not yet exist. Indexing genome now.
1583s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1583s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s bt2 index files: $VAR1 = [];
1583s Note - bowtie-build indices do not yet exist. Indexing genome now.
1583s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1583s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1583s 2128 reads; of these:
1583s   2128 (100.00%) were unpaired; of these:
1583s     6 (0.28%) aligned 0 times
1583s     1722 (80.92%) aligned exactly 1 time
1583s     400 (18.80%) aligned >1 times
1583s 99.72% overall alignment rate
1583s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s 34 reads; of these:
1583s   34 (100.00%) were unpaired; of these:
1583s     1 (2.94%) aligned 0 times
1583s     33 (97.06%) aligned exactly 1 time
1583s     0 (0.00%) aligned >1 times
1583s 97.06% overall alignment rate
1583s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s 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
1583s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s 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 
1583s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s 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
1583s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1583s 
1583s 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 
1583s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1583s 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
1583s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s 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
1583s 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 
1583s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1583s 
1583s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1583s -processing jaccard pair sensor
1583s 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
1583s 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
1583s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1583s 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
1583s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1583s 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
1583s 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 
1583s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1583s -processing jaccard pair sensor
1583s 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
1583s 
[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
1583s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1585s 
succeeded(21)   39.6226% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1585s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1585s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1585s bt2 index files: $VAR1 = [];
1585s Note - bowtie-build indices do not yet exist. Indexing genome now.
1585s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1585s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1585s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1586s 2557 reads; of these:
1586s   2557 (100.00%) were unpaired; of these:
1586s     11 (0.43%) aligned 0 times
1586s     1332 (52.09%) aligned exactly 1 time
1586s     1214 (47.48%) aligned >1 times
1586s 99.57% overall alignment rate
1586s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1586s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1586s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1586s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1586s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1586s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1586s 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
1586s 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 
1586s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1586s 
1586s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1586s 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
1586s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1586s 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
1586s 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 
1586s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1586s -processing jaccard pair sensor
1586s 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
1586s 
[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
1587s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1588s 
succeeded(22)   41.5094% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1588s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1588s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1588s bt2 index files: $VAR1 = [];
1588s Note - bowtie-build indices do not yet exist. Indexing genome now.
1588s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1589s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1589s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1589s 5664 reads; of these:
1589s   5664 (100.00%) were unpaired; of these:
1589s     8 (0.14%) aligned 0 times
1589s     3217 (56.80%) aligned exactly 1 time
1589s     2439 (43.06%) aligned >1 times
1589s 99.86% overall alignment rate
1589s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1589s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1590s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1590s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1590s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1590s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1590s 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
1590s 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 
1590s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1590s 
1590s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1590s 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
1590s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1590s 
succeeded(23)   43.3962% completed.    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
1590s 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 
1590s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1590s -processing jaccard pair sensor
1590s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1590s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1590s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1590s bt2 index files: $VAR1 = [];
1590s Note - bowtie-build indices do not yet exist. Indexing genome now.
1590s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1590s 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
1590s 
[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
1590s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1591s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1591s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1591s 907 reads; of these:
1591s   907 (100.00%) were unpaired; of these:
1591s     2 (0.22%) aligned 0 times
1591s     839 (92.50%) aligned exactly 1 time
1591s     66 (7.28%) aligned >1 times
1591s 99.78% overall alignment rate
1591s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1591s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1591s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1591s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1591s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1591s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1591s 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
1591s 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 
1591s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1591s 
1591s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1591s 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
1591s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1591s 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
1591s 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 
1591s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1591s -processing jaccard pair sensor
1591s 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
1591s 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
1591s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1595s 
succeeded(24)   45.283% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1595s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1595s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1595s bt2 index files: $VAR1 = [];
1595s Note - bowtie-build indices do not yet exist. Indexing genome now.
1595s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1595s 
succeeded(25)   47.1698% completed.    CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1595s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1596s 46 reads; of these:
1596s   46 (100.00%) were unpaired; of these:
1596s     0 (0.00%) aligned 0 times
1596s     44 (95.65%) aligned exactly 1 time
1596s     2 (4.35%) aligned >1 times
1596s 100.00% overall alignment rate
1596s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s 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
1596s 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 
1596s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1596s 
1596s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1596s 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
1596s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s 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
1596s 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 
1596s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1596s -processing jaccard pair sensor
1596s 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
1596s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1596s 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
1596s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s bt2 index files: $VAR1 = [];
1596s Note - bowtie-build indices do not yet exist. Indexing genome now.
1596s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1596s 1717 reads; of these:
1596s   1717 (100.00%) were unpaired; of these:
1596s     1 (0.06%) aligned 0 times
1596s     1511 (88.00%) aligned exactly 1 time
1596s     205 (11.94%) aligned >1 times
1596s 99.94% overall alignment rate
1596s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s 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
1596s 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 
1596s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1596s 
1596s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1596s 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
1596s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1596s 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
1596s 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 
1596s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1596s -processing jaccard pair sensor
1596s 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
1597s 
[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
1597s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1598s 
succeeded(26)   49.0566% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1598s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1598s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1598s bt2 index files: $VAR1 = [];
1598s Note - bowtie-build indices do not yet exist. Indexing genome now.
1598s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1598s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1598s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1598s 85 reads; of these:
1598s   85 (100.00%) were unpaired; of these:
1598s     3 (3.53%) aligned 0 times
1598s     82 (96.47%) aligned exactly 1 time
1598s     0 (0.00%) aligned >1 times
1598s 96.47% overall alignment rate
1598s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1598s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1598s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1598s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1598s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1598s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1598s 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
1598s 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 
1598s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1598s 
1598s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1598s 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
1598s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1598s 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
1598s 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 
1598s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1598s -processing jaccard pair sensor
1598s 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
1599s 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
1599s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1600s 
succeeded(27)   50.9434% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1600s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1600s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1600s bt2 index files: $VAR1 = [];
1600s Note - bowtie-build indices do not yet exist. Indexing genome now.
1600s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1600s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1600s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1600s 54 reads; of these:
1600s   54 (100.00%) were unpaired; of these:
1600s     9 (16.67%) aligned 0 times
1600s     45 (83.33%) aligned exactly 1 time
1600s     0 (0.00%) aligned >1 times
1600s 83.33% overall alignment rate
1600s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1600s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1601s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1601s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1601s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1601s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1601s 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
1601s 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 
1601s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1601s 
1601s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1601s 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
1601s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1601s 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
1601s 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 
1601s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1601s -processing jaccard pair sensor
1601s 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
1601s 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
1601s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1601s 
succeeded(28)   52.8302% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1601s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1601s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1601s bt2 index files: $VAR1 = [];
1601s Note - bowtie-build indices do not yet exist. Indexing genome now.
1601s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1601s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1601s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1601s 18 reads; of these:
1601s   18 (100.00%) were unpaired; of these:
1601s     5 (27.78%) aligned 0 times
1601s     13 (72.22%) aligned exactly 1 time
1601s     0 (0.00%) aligned >1 times
1601s 72.22% overall alignment rate
1601s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1601s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1601s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1601s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1601s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1601s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1601s 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
1601s 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 
1602s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1602s 
1602s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1602s 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
1602s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1602s 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
1602s 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 
1602s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1602s -processing jaccard pair sensor
1602s 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
1602s 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
1602s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1602s 
succeeded(29)   54.717% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1602s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1602s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1602s bt2 index files: $VAR1 = [];
1602s Note - bowtie-build indices do not yet exist. Indexing genome now.
1602s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1602s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1602s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1603s 
succeeded(30)   56.6038% completed.    277 reads; of these:
1603s   277 (100.00%) were unpaired; of these:
1603s     0 (0.00%) aligned 0 times
1603s     277 (100.00%) aligned exactly 1 time
1603s     0 (0.00%) aligned >1 times
1603s 100.00% overall alignment rate
1603s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s 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
1603s 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 
1603s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1603s 
1603s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1603s 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
1603s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s 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
1603s 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 
1603s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1603s -processing jaccard pair sensor
1603s 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
1603s 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
1603s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1603s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s bt2 index files: $VAR1 = [];
1603s Note - bowtie-build indices do not yet exist. Indexing genome now.
1603s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1603s 20 reads; of these:
1603s   20 (100.00%) were unpaired; of these:
1603s     4 (20.00%) aligned 0 times
1603s     16 (80.00%) aligned exactly 1 time
1603s     0 (0.00%) aligned >1 times
1603s 80.00% overall alignment rate
1603s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s 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
1603s 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 
1603s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1603s 
1603s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1603s 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
1603s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1603s 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
1603s 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 
1603s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1603s -processing jaccard pair sensor
1603s 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
1603s 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
1603s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1605s 
succeeded(31)   58.4906% completed.    
succeeded(32)   60.3774% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1605s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1605s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1605s bt2 index files: $VAR1 = [];
1605s Note - bowtie-build indices do not yet exist. Indexing genome now.
1605s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1605s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1605s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1605s 20 reads; of these:
1605s   20 (100.00%) were unpaired; of these:
1605s     12 (60.00%) aligned 0 times
1605s     8 (40.00%) aligned exactly 1 time
1605s     0 (0.00%) aligned >1 times
1605s 40.00% overall alignment rate
1606s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1606s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s 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
1606s 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 
1606s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s bt2 index files: $VAR1 = [];
1606s Note - bowtie-build indices do not yet exist. Indexing genome now.
1606s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1606s 
1606s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1606s 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
1606s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s 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
1606s 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 
1606s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1606s -processing jaccard pair sensor
1606s 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
1606s 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
1606s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1606s 77 reads; of these:
1606s   77 (100.00%) were unpaired; of these:
1606s     2 (2.60%) aligned 0 times
1606s     75 (97.40%) aligned exactly 1 time
1606s     0 (0.00%) aligned >1 times
1606s 97.40% overall alignment rate
1606s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s 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
1606s 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 
1606s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1606s 
1606s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1606s 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
1606s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1606s 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
1606s 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 
1606s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1606s -processing jaccard pair sensor
1606s 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
1606s 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
1606s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1607s 
succeeded(33)   62.2641% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1607s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1607s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1607s bt2 index files: $VAR1 = [];
1607s Note - bowtie-build indices do not yet exist. Indexing genome now.
1607s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1607s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1607s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1607s 52 reads; of these:
1607s   52 (100.00%) were unpaired; of these:
1607s     5 (9.62%) aligned 0 times
1607s     47 (90.38%) aligned exactly 1 time
1607s     0 (0.00%) aligned >1 times
1607s 90.38% overall alignment rate
1607s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1607s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1607s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1607s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1607s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1607s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1607s 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
1607s 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 
1607s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1607s 
1607s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1607s 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
1607s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1607s 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
1607s 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 
1607s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1607s -processing jaccard pair sensor
1607s 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
1607s 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
1608s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1608s 
succeeded(34)   64.1509% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1608s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1608s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1608s bt2 index files: $VAR1 = [];
1608s Note - bowtie-build indices do not yet exist. Indexing genome now.
1608s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1608s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1608s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1609s 115 reads; of these:
1609s   115 (100.00%) were unpaired; of these:
1609s     6 (5.22%) aligned 0 times
1609s     109 (94.78%) aligned exactly 1 time
1609s     0 (0.00%) aligned >1 times
1609s 94.78% overall alignment rate
1609s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1609s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1609s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1609s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1609s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1609s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1609s 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
1609s 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 
1609s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1609s 
1609s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1609s 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
1609s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1609s 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
1609s 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 
1609s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1609s -processing jaccard pair sensor
1609s 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
1609s 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
1609s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1610s 
succeeded(35)   66.0377% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1610s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1610s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1610s bt2 index files: $VAR1 = [];
1610s Note - bowtie-build indices do not yet exist. Indexing genome now.
1610s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1610s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1610s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1611s 4380 reads; of these:
1611s   4380 (100.00%) were unpaired; of these:
1611s     10 (0.23%) aligned 0 times
1611s     2462 (56.21%) aligned exactly 1 time
1611s     1908 (43.56%) aligned >1 times
1611s 99.77% overall alignment rate
1611s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1611s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1611s 
succeeded(36)   67.9245% completed.    CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1611s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1611s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1611s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1611s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1611s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1611s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1611s 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
1611s 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 
1611s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1611s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1611s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1611s 
1611s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1611s bt2 index files: $VAR1 = [];
1611s Note - bowtie-build indices do not yet exist. Indexing genome now.
1611s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1611s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1611s 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
1612s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1612s 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
1612s 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 
1612s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1612s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1612s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1612s -processing jaccard pair sensor
1612s 371 reads; of these:
1612s   371 (100.00%) were unpaired; of these:
1612s     2 (0.54%) aligned 0 times
1612s     296 (79.78%) aligned exactly 1 time
1612s     73 (19.68%) aligned >1 times
1612s 99.46% overall alignment rate
1612s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1612s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1612s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1612s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1612s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1612s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1612s 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
1612s 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 
1612s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1612s 
1612s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1612s 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
1612s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1612s 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
1612s 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 
1612s 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
1612s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1612s -processing jaccard pair sensor
1612s 
[1000 lines read]  scaff:a1;135 lend:78  rend:364     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
1612s 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
1612s 
[2000 lines read]  scaff:a1;135 lend:614  rend:934     
[3000 lines read]  scaff:a20;2 lend:7  rend:49     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1612s 
[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
1612s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1615s 
succeeded(37)   69.8113% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1615s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1615s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1615s bt2 index files: $VAR1 = [];
1615s Note - bowtie-build indices do not yet exist. Indexing genome now.
1615s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1615s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1615s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1615s 16 reads; of these:
1615s   16 (100.00%) were unpaired; of these:
1615s     0 (0.00%) aligned 0 times
1615s     14 (87.50%) aligned exactly 1 time
1615s     2 (12.50%) aligned >1 times
1615s 100.00% overall alignment rate
1615s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1615s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1615s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1615s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1615s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1615s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1615s 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
1615s 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 
1615s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1615s 
1615s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1615s 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
1615s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1615s 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
1615s 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 
1615s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1615s -processing jaccard pair sensor
1615s 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
1615s 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
1615s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1616s 
succeeded(38)   71.6981% completed.    
succeeded(39)   73.5849% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1616s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1616s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1616s bt2 index files: $VAR1 = [];
1616s Note - bowtie-build indices do not yet exist. Indexing genome now.
1616s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1616s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1616s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1616s 70 reads; of these:
1616s   70 (100.00%) were unpaired; of these:
1616s     10 (14.29%) aligned 0 times
1616s     59 (84.29%) aligned exactly 1 time
1616s     1 (1.43%) aligned >1 times
1616s 85.71% overall alignment rate
1616s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1616s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1616s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1616s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1616s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1616s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1616s 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
1616s 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 
1617s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1617s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1617s 
1617s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1617s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1617s 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
1617s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1617s 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
1617s 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 
1617s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1617s bt2 index files: $VAR1 = [];
1617s Note - bowtie-build indices do not yet exist. Indexing genome now.
1617s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1617s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1617s -processing jaccard pair sensor
1617s 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
1617s 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
1617s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1617s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1617s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1617s 5953 reads; of these:
1617s   5953 (100.00%) were unpaired; of these:
1617s     11 (0.18%) aligned 0 times
1617s     3807 (63.95%) aligned exactly 1 time
1617s     2135 (35.86%) aligned >1 times
1617s 99.82% overall alignment rate
1617s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1617s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1618s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1618s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1618s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1618s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1618s 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
1618s 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 
1618s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1618s 
1618s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1618s 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
1618s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1618s 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
1618s 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 
1618s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1618s -processing jaccard pair sensor
1618s 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
1619s 
[1000 lines read]  scaff:a1;90 lend:143  rend:454     
[2000 lines read]  scaff:a1;90 lend:1115  rend:1442     
[3000 lines read]  scaff:a1;90 lend:1905  rend:2258     
[4000 lines read]  scaff:a21;2 lend:5  rend:43     
[5000 lines read]  scaff:a39;2 lend:10  rend:46     CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl --jaccard_wig bowtie_alignments.for_jaccard.bam.J100.wig --coverage_wig bowtie_alignments.for_jaccard.bam.frag_coords.wig  > bowtie_alignments.for_jaccard.bam.J100.wig.clips
1619s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1619s 
succeeded(40)   75.4717% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1619s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1619s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1619s bt2 index files: $VAR1 = [];
1619s Note - bowtie-build indices do not yet exist. Indexing genome now.
1619s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1620s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1620s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1620s 454 reads; of these:
1620s   454 (100.00%) were unpaired; of these:
1620s     1 (0.22%) aligned 0 times
1620s     368 (81.06%) aligned exactly 1 time
1620s     85 (18.72%) aligned >1 times
1620s 99.78% overall alignment rate
1620s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1620s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1620s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1620s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1620s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1620s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1620s 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
1620s 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 
1620s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1620s 
1620s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1620s 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
1620s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1620s 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
1620s 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 
1620s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1620s -processing jaccard pair sensor
1620s 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
1620s 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
1620s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1624s 
succeeded(41)   77.3585% completed.    
succeeded(42)   79.2453% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1624s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1624s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1624s bt2 index files: $VAR1 = [];
1624s Note - bowtie-build indices do not yet exist. Indexing genome now.
1624s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1624s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1624s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1624s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1624s bt2 index files: $VAR1 = [];
1624s Note - bowtie-build indices do not yet exist. Indexing genome now.
1624s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1624s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1624s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1624s 997 reads; of these:
1624s   997 (100.00%) were unpaired; of these:
1624s     3 (0.30%) aligned 0 times
1624s     568 (56.97%) aligned exactly 1 time
1624s     426 (42.73%) aligned >1 times
1624s 99.70% overall alignment rate
1624s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1624s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1624s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1625s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1625s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1625s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1625s 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
1625s 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 
1625s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1625s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1625s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1625s 
1625s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1625s 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
1625s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1625s 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
1625s 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 
1625s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1625s -processing jaccard pair sensor
1625s 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
1625s 1733 reads; of these:
1625s   1733 (100.00%) were unpaired; of these:
1625s     0 (0.00%) aligned 0 times
1625s     794 (45.82%) aligned exactly 1 time
1625s     939 (54.18%) aligned >1 times
1625s 100.00% overall alignment rate
1625s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1625s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1625s 
[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
1625s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1625s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1625s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1625s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1625s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1625s 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
1625s 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 
1625s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1625s 
1625s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1625s 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
1625s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1625s 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
1625s 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 
1625s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1625s -processing jaccard pair sensor
1625s 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
1625s 
[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
1625s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1629s 
succeeded(43)   81.1321% completed.    
succeeded(44)   83.0189% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1629s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1629s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1629s bt2 index files: $VAR1 = [];
1629s Note - bowtie-build indices do not yet exist. Indexing genome now.
1629s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1629s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1629s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1629s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1629s bt2 index files: $VAR1 = [];
1629s Note - bowtie-build indices do not yet exist. Indexing genome now.
1629s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1629s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1629s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1629s 538 reads; of these:
1629s   538 (100.00%) were unpaired; of these:
1629s     2 (0.37%) aligned 0 times
1629s     530 (98.51%) aligned exactly 1 time
1629s     6 (1.12%) aligned >1 times
1629s 99.63% overall alignment rate
1629s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1629s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1629s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1629s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1629s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1629s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1629s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1629s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1629s 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
1629s 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 
1629s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1629s 
1629s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1629s 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
1629s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1629s 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
1629s 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 
1629s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1629s -processing jaccard pair sensor
1629s 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
1629s 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
1629s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1630s 3962 reads; of these:
1630s   3962 (100.00%) were unpaired; of these:
1630s     2 (0.05%) aligned 0 times
1630s     2253 (56.87%) aligned exactly 1 time
1630s     1707 (43.08%) aligned >1 times
1630s 99.95% overall alignment rate
1630s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1630s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1630s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1630s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1630s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1630s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1630s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1630s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1630s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1630s 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
1630s 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 
1630s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1630s 
1630s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1630s 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
1630s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1630s 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
1630s 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 
1630s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1630s -processing jaccard pair sensor
1630s 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
1630s 
[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
1630s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1633s 
succeeded(45)   84.9057% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1633s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1633s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1633s bt2 index files: $VAR1 = [];
1633s Note - bowtie-build indices do not yet exist. Indexing genome now.
1633s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1633s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1633s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1634s 
succeeded(46)   86.7924% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1634s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1634s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1634s bt2 index files: $VAR1 = [];
1634s Note - bowtie-build indices do not yet exist. Indexing genome now.
1634s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1634s 7038 reads; of these:
1634s   7038 (100.00%) were unpaired; of these:
1634s     25 (0.36%) aligned 0 times
1634s     2368 (33.65%) aligned exactly 1 time
1634s     4645 (66.00%) aligned >1 times
1634s 99.64% overall alignment rate
1634s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1634s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1634s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1634s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1634s 213 reads; of these:
1634s   213 (100.00%) were unpaired; of these:
1635s     1 (0.47%) aligned 0 times
1635s     121 (56.81%) aligned exactly 1 time
1635s     91 (42.72%) aligned >1 times
1635s 99.53% overall alignment rate
1635s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1635s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1635s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1635s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1635s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1635s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1635s 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
1635s 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 
1635s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1635s 
1635s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1635s 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
1635s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1635s 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
1635s 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 
1635s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1635s -processing jaccard pair sensor
1635s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1635s 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
1635s 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
1635s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1635s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1635s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1635s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1635s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1635s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1635s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1635s 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
1635s 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 
1635s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1635s 
1635s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1635s 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
1635s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1635s 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
1635s 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 
1635s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1635s -processing jaccard pair sensor
1636s 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
1636s 
[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
1636s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1638s 
succeeded(47)   88.6792% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1638s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1638s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1638s bt2 index files: $VAR1 = [];
1638s Note - bowtie-build indices do not yet exist. Indexing genome now.
1638s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1638s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1638s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1638s 51 reads; of these:
1638s   51 (100.00%) were unpaired; of these:
1638s     4 (7.84%) aligned 0 times
1638s     47 (92.16%) aligned exactly 1 time
1638s     0 (0.00%) aligned >1 times
1638s 92.16% overall alignment rate
1638s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1638s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1638s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1638s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1638s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1638s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1638s 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
1638s 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 
1638s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1638s 
1638s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1638s 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
1638s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1638s 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
1638s 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 
1639s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1639s -processing jaccard pair sensor
1639s 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
1639s 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
1639s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1641s 
succeeded(48)   90.566% completed.    
succeeded(49)   92.4528% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1641s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1641s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1641s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1641s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1641s bt2 index files: $VAR1 = [];
1641s Note - bowtie-build indices do not yet exist. Indexing genome now.
1641s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1641s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1641s bt2 index files: $VAR1 = [];
1641s Note - bowtie-build indices do not yet exist. Indexing genome now.
1641s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1641s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1641s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1641s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1641s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1641s 10 reads; of these:
1641s   10 (100.00%) were unpaired; of these:
1641s     5 (50.00%) aligned 0 times
1641s     5 (50.00%) aligned exactly 1 time
1641s     0 (0.00%) aligned >1 times
1641s 50.00% overall alignment rate
1642s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1642s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1642s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1642s 10 reads; of these:
1642s   10 (100.00%) were unpaired; of these:
1642s     2 (20.00%) aligned 0 times
1642s     8 (80.00%) aligned exactly 1 time
1642s     0 (0.00%) aligned >1 times
1642s 80.00% overall alignment rate
1642s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1642s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1642s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1642s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1642s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1642s 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
1642s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1642s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1642s 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 
1642s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1642s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1642s 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
1642s 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 
1642s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1642s 
1642s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1642s 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
1642s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1642s 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
1642s 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 
1642s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1642s 
1642s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1642s 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
1642s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1642s 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
1642s 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 
1642s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1642s -processing jaccard pair sensor
1642s 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
1642s 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
1642s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1642s -processing jaccard pair sensor
1642s 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
1642s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1642s 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
1642s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s 
succeeded(50)   94.3396% completed.    
succeeded(51)   96.2264% completed.    CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1643s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s CMD: /usr/lib/trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl --seqType fa --single /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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 
1643s bt2 index files: $VAR1 = [];
1643s Note - bowtie-build indices do not yet exist. Indexing genome now.
1643s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s CMD: samtools faidx /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s bt2 index files: $VAR1 = [];
1643s Note - bowtie-build indices do not yet exist. Indexing genome now.
1643s CMD: bowtie2-build -q /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1643s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s CMD: bash -c "set -o pipefail; bowtie2 --local -k 20 --threads 1 --no-unal -f -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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" 
1643s 30 reads; of these:
1643s   30 (100.00%) were unpaired; of these:
1643s     9 (30.00%) aligned 0 times
1643s     21 (70.00%) aligned exactly 1 time
1643s     0 (0.00%) aligned >1 times
1643s 70.00% overall alignment rate
1643s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s 26 reads; of these:
1643s   26 (100.00%) were unpaired; of these:
1643s     0 (0.00%) aligned 0 times
1643s     26 (100.00%) aligned exactly 1 time
1643s     0 (0.00%) aligned >1 times
1643s 100.00% overall alignment rate
1643s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s CMD: /usr/lib/trinityrnaseq/util/support_scripts/SAM_strand_separator.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s 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
1643s CMD: samtools view -bt /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s 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 
1643s CMD: samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s -cleaning up and removing intermediate file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s 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
1643s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1643s 
1643s 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 
1643s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1643s 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
1643s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s 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
1643s 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 
1643s -extracting read coordinates from bowtie_alignments.for_jaccard.bam into bowtie_alignments.for_jaccard.bam.read_coords
1643s 
1643s CMD: touch bowtie_alignments.for_jaccard.bam.read_coords.ok
1643s 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
1643s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1643s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s -processing jaccard pair sensor
1643s 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
1643s 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
1643s 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 
1643s 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
1643s CMD: sort -T . -k1,1 -k4,4n bowtie_alignments.for_jaccard.bam.frag_coords > bowtie_alignments.for_jaccard.bam.frag_coords.sort_by_rend
1643s -processing jaccard pair sensor
1643s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1643s 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
1643s 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
1643s CMD: /usr/lib/trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/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
1645s 
succeeded(52)   98.1132% completed.    
succeeded(53)   100% completed.    
1645s 
1645s All commands completed successfully. :-)
1645s 
1645s Friday, November 1, 2024: 10:36:00	CMD: find Dir_*  -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta.tmp
1645s Friday, November 1, 2024: 10:36:00	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta.gene_trans_map
1645s 
1645s 
1645s Finished. See /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta for reconstructed transcripts
1645s 
1645s 
1645s outfile="test_Schizo_trinityGG_jaccard_RF_outdir/Trinity-GG.fasta"
1645s asmsize=$(wc -c <"${outfile}")
1645s if [ $asmsize -le 50000 ]; then
1645s     echo "Error, ${outfile} potentially incomplete"
1645s     exit 1
1645s else
1645s     echo "ok"
1645s     exit 0
1645s fi
1645s ok
1645s ./run_small_GG_mutliScaff_test.sh
1645s #!/bin/bash -ve
1645s 
1645s 
1645s $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
1645s 
1645s 
1645s      ______  ____   ____  ____   ____  ______  __ __
1645s     |      ||    \ |    ||    \ |    ||      ||  |  |
1645s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1645s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1645s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1645s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1645s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1645s 
1645s     Trinity-v2.15.1
1645s 
1645s 
1645s 
1645s Friday, November 1, 2024: 10:36:00	CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl transAligns.cSorted.bam
1645s -appears to be a coordinate sorted bam file. ok.
1645s Friday, November 1, 2024: 10:36:00	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir
1645s 
1645s 
1645s ----------------------------------------------------------------------------------
1645s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1645s ----------------------------------------------------------------------------------
1645s 
1645s -found paired-end aligned read. Running in paired-end mode.
1645s Friday, November 1, 2024: 10:36:00	CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/transAligns.cSorted.bam
1647s Done with chr TRINITY_DN0_c0_g1_i1.
1647s Done with chr TRINITY_DN10_c0_g1_i1.
1647s Done with chr TRINITY_DN12_c0_g1_i1.
1647s Done with chr TRINITY_DN12_c0_g1_i2.
1647s Done with chr TRINITY_DN14_c0_g1_i1.
1647s Done with chr TRINITY_DN14_c0_g2_i1.
1647s Done with chr TRINITY_DN15_c0_g1_i1.
1647s Done with chr TRINITY_DN16_c0_g1_i1.
1647s Done with chr TRINITY_DN16_c0_g2_i1.
1647s Done with chr TRINITY_DN18_c0_g1_i1.
1647s Done with chr TRINITY_DN18_c0_g1_i2.
1647s Done with chr TRINITY_DN19_c0_g1_i1.
1647s Done with chr TRINITY_DN20_c0_g1_i1.
1647s Done with chr TRINITY_DN20_c0_g2_i1.
1647s Done with chr TRINITY_DN20_c0_g1_i2.
1647s Done with chr TRINITY_DN20_c0_g1_i3.
1647s Done with chr TRINITY_DN20_c0_g1_i4.
1647s Done with chr TRINITY_DN20_c0_g1_i5.
1647s Done with chr TRINITY_DN20_c0_g1_i6.
1647s Done with chr TRINITY_DN20_c0_g1_i7.
1647s Done with chr TRINITY_DN21_c0_g1_i1.
1647s Done with chr TRINITY_DN21_c0_g1_i2.
1647s Done with chr TRINITY_DN22_c0_g1_i1.
1647s Done with chr TRINITY_DN22_c0_g2_i1.
1647s Done with chr TRINITY_DN22_c0_g3_i1.
1647s Done with chr TRINITY_DN22_c0_g4_i1.
1647s Done with chr TRINITY_DN22_c0_g3_i2.
1647s Done with chr TRINITY_DN22_c0_g3_i3.
1647s Done with chr TRINITY_DN22_c0_g3_i4.
1647s Done with chr TRINITY_DN22_c0_g5_i1.
1647s Done with chr TRINITY_DN22_c0_g6_i1.
1647s Done with chr TRINITY_DN22_c0_g3_i5.
1647s Done with chr TRINITY_DN22_c0_g7_i1.
1647s Done with chr TRINITY_DN23_c0_g1_i1.
1647s Done with chr TRINITY_DN23_c0_g2_i1.
1647s Done with chr TRINITY_DN23_c0_g1_i2.
1647s Done with chr TRINITY_DN23_c0_g3_i1.
1647s Done with chr TRINITY_DN23_c0_g4_i1.
1647s Done with chr TRINITY_DN23_c0_g5_i1.
1647s Done with chr TRINITY_DN23_c0_g1_i3.
1647s Done with chr TRINITY_DN23_c0_g1_i4.
1647s Done with chr TRINITY_DN24_c0_g1_i1.
1647s Done with chr TRINITY_DN24_c0_g2_i1.
1647s Done with chr TRINITY_DN24_c0_g3_i1.
1647s Done with chr TRINITY_DN24_c0_g3_i2.
1647s Done with chr TRINITY_DN25_c1_g1_i1.
1647s Done with chr TRINITY_DN25_c1_g1_i2.
1647s Done with chr TRINITY_DN25_c1_g1_i3.
1647s Done with chr TRINITY_DN25_c1_g1_i4.
1647s Done with chr TRINITY_DN25_c1_g1_i5.
1647s Done with chr TRINITY_DN26_c0_g1_i1.
1647s Done with chr TRINITY_DN26_c0_g1_i2.
1647s Done with chr TRINITY_DN26_c1_g1_i1.
1647s Done with chr TRINITY_DN26_c1_g1_i2.
1647s Done with chr TRINITY_DN26_c1_g1_i3.
1647s Done with chr TRINITY_DN26_c1_g1_i4.
1647s Done with chr TRINITY_DN26_c1_g1_i5.
1647s Done with chr TRINITY_DN26_c1_g1_i6.
1647s Done with chr TRINITY_DN26_c1_g2_i1.
1647s Done with chr TRINITY_DN26_c1_g1_i7.
1647s Done with chr TRINITY_DN26_c1_g3_i1.
1647s Done with chr TRINITY_DN26_c1_g1_i8.
1647s Done with chr TRINITY_DN26_c1_g1_i9.
1647s Done with chr TRINITY_DN26_c1_g1_i10.
1647s Done with chr TRINITY_DN26_c1_g1_i11.
1647s Done with chr TRINITY_DN26_c1_g3_i2.
1647s Done with chr TRINITY_DN26_c1_g1_i12.
1647s Done with chr TRINITY_DN26_c1_g4_i1.
1647s Done with chr TRINITY_DN26_c1_g1_i13.
1647s Done with chr TRINITY_DN26_c1_g1_i14.
1647s Done with chr TRINITY_DN26_c1_g1_i15.
1647s Done with chr TRINITY_DN26_c1_g1_i16.
1647s Done with chr TRINITY_DN26_c1_g1_i17.
1647s Done with chr TRINITY_DN26_c1_g1_i18.
1647s Done with chr TRINITY_DN26_c1_g3_i3.
1647s Done with chr TRINITY_DN26_c1_g1_i19.
1647s Done with chr TRINITY_DN26_c1_g3_i4.
1647s Done with chr TRINITY_DN26_c1_g5_i1.
1647s Done with chr TRINITY_DN26_c1_g1_i20.
1647s Done with chr TRINITY_DN26_c1_g1_i21.
1647s Done with chr TRINITY_DN26_c1_g3_i5.
1647s Done with chr TRINITY_DN26_c2_g1_i1.
1647s Done with chr TRINITY_DN26_c2_g1_i2.
1647s Done with chr TRINITY_DN26_c2_g2_i1.
1647s Done with chr TRINITY_DN26_c2_g3_i1.
1647s Done with chr TRINITY_DN26_c2_g1_i3.
1647s Done with chr TRINITY_DN26_c2_g1_i4.
1647s Done with chr TRINITY_DN26_c2_g1_i5.
1647s Done with chr TRINITY_DN27_c0_g1_i1.
1647s Done with chr TRINITY_DN4_c0_g1_i1.
1647s Done with chr TRINITY_DN5_c0_g1_i1.
1647s Friday, November 1, 2024: 10:36:02	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/transAligns.cSorted.bam.norm_200.bam.ok
1647s Friday, November 1, 2024: 10:36:02	CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.xkSdGF/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 
1647s 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 
1647s -extracting read coordinates from transAligns.cSorted.bam.norm_200.bam into transAligns.cSorted.bam.norm_200.bam.read_coords
1647s 
1652s CMD: touch transAligns.cSorted.bam.norm_200.bam.read_coords.ok
1652s 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
1653s CMD: cp /tmp/autopkgtest.xkSdGF/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.xkSdGF/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
1653s 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
1654s 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
1657s 
[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
1657s 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
1657s CMD: touch transAligns.cSorted.bam.norm_200.bam.minC1.gff.ok
1657s 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 
1657s // parsing paritions.
1657s 
[92]  -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN0_c0_g1_i1/0/1_251.trinity.reads
1657s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN10_c0_g1_i1/0/1_307.trinity.reads
1657s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN12_c0_g1_i1/0/1_246.trinity.reads
1657s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN12_c0_g1_i2/0/1_312.trinity.reads
1657s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN14_c0_g1_i1/0/1_280.trinity.reads
1657s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN14_c0_g2_i1/0/1_390.trinity.reads
1657s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN15_c0_g1_i1/0/1_239.trinity.reads
1657s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN16_c0_g1_i1/0/1_272.trinity.reads
1657s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN16_c0_g2_i1/0/1_324.trinity.reads
1657s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN18_c0_g1_i1/0/36_344.trinity.reads
1657s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN18_c0_g1_i2/0/36_348.trinity.reads
1657s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN19_c0_g1_i1/0/1_304.trinity.reads
1657s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i1/0/1_769.trinity.reads
1657s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g2_i1/0/1_484.trinity.reads
1657s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i2/0/3_2306.trinity.reads
1657s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i3/0/1_2226.trinity.reads
1657s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i4/0/1_2619.trinity.reads
1657s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i5/0/1_1442.trinity.reads
1657s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i6/0/1_1946.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN20_c0_g1_i7/0/1_2899.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN21_c0_g1_i1/0/1_2802.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN21_c0_g1_i2/0/1_3823.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g1_i1/0/1_422.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g2_i1/0/1_204.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i1/0/1_2433.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g4_i1/0/1_219.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i2/0/1_790.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i3/0/1_2269.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i4/0/1_2200.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g5_i1/0/1_590.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g6_i1/0/1_246.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g3_i5/0/1_2364.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN22_c0_g7_i1/0/1_513.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i1/0/1_799.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g2_i1/0/1_205.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i2/0/1_2592.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g3_i1/0/1_289.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g4_i1/0/1_341.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g5_i1/0/1_952.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i3/0/1_2514.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN23_c0_g1_i4/0/1_296.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g1_i1/0/1_205.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g2_i1/0/1_433.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g3_i1/0/3_7194.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN24_c0_g3_i2/0/2_530.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i1/0/1_1375.trinity.reads
1658s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i2/0/1_3516.trinity.reads
1659s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i3/0/1_3667.trinity.reads
1659s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i4/0/1_3625.trinity.reads
1659s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN25_c1_g1_i5/0/1_220.trinity.reads
1659s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c0_g1_i1/0/1_5399.trinity.reads
1659s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c0_g1_i2/0/1_5528.trinity.reads
1659s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i1/0/1_8158.trinity.reads
1659s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i2/0/1_8134.trinity.reads
1660s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i3/0/1_8130.trinity.reads
1660s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i4/0/1_8138.trinity.reads
1660s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i5/0/1_8087.trinity.reads
1660s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i6/0/1_8146.trinity.reads
1660s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g2_i1/0/1_341.trinity.reads
1660s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i7/0/1_8091.trinity.reads
1660s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i1/0/1_5713.trinity.reads
1660s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i8/0/1_8079.trinity.reads
1661s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i9/0/1_8122.trinity.reads
1661s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i10/0/1_8150.trinity.reads
1661s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i11/0/1_6104.trinity.reads
1661s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i2/0/1_5905.trinity.reads
1661s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i12/0/1_8130.trinity.reads
1661s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g4_i1/0/1_298.trinity.reads
1661s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i13/0/1_8126.trinity.reads
1661s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i14/0/1_8091.trinity.reads
1662s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i15/0/1_8095.trinity.reads
1662s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i16/0/1_8150.trinity.reads
1662s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i17/0/1_8142.trinity.reads
1662s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i18/0/1_8099.trinity.reads
1662s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i3/0/1_3101.trinity.reads
1662s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i19/0/1_6546.trinity.reads
1662s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i4/0/1_5854.trinity.reads
1663s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g5_i1/0/1_215.trinity.reads
1663s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i20/0/1_8154.trinity.reads
1663s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g1_i21/0/1_6129.trinity.reads
1663s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c1_g3_i5/0/1_3918.trinity.reads
1663s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i1/0/1_8817.trinity.reads
1663s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i2/0/44_633.trinity.reads
1663s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g2_i1/0/1_281.trinity.reads
1663s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g3_i1/0/1_491.trinity.reads
1663s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i3/0/1_8757.trinity.reads
1663s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i4/0/1_6795.trinity.reads
1663s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN26_c2_g1_i5/0/1_8973.trinity.reads
1663s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN27_c0_g1_i1/0/1_261.trinity.reads
1663s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN4_c0_g1_i1/0/1_329.trinity.reads
1663s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN5_c0_g1_i1/0/1_252.trinity.reads
1663s -writing to Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff/TRINITY_DN7_c0_g1_i1/0/1_301.trinity.reads
1663s CMD: touch Dir_transAligns.cSorted.bam.norm_200.bam.minC1.gff.ok
1663s ##
1663s Done
1663s ##
1663s 
1664s Friday, November 1, 2024: 10:36:18	CMD: touch partitions.ok
1664s Friday, November 1, 2024: 10:36:18	CMD: find Dir_* -name '*reads' > read_files.list
1664s Friday, November 1, 2024: 10:36:18	CMD: touch read_files.list.ok
1664s Friday, November 1, 2024: 10:36:18	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
1664s Friday, November 1, 2024: 10:36:19	CMD: touch trinity_GG.cmds.ok
1664s Friday, November 1, 2024: 10:36:19	CMD: touch trinity_GG.cmds.ok
1664s 
1664s 
1664s --------------------------------------------------------------------------------
1664s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1664s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1664s --------------------------------------------------------------------------------
1664s 
1664s Friday, November 1, 2024: 10:36:19	CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -v -shuffle 
1664s Number of Commands: 85
1902s 
succeeded(1)   1.17647% completed.    
succeeded(2)   2.35294% completed.    
succeeded(3)   3.52941% completed.    
succeeded(4)   4.70588% completed.    
succeeded(5)   5.88235% completed.    
succeeded(6)   7.05882% completed.    
succeeded(7)   8.23529% completed.    
succeeded(8)   9.41177% completed.    
succeeded(9)   10.5882% completed.    
succeeded(10)   11.7647% completed.    
succeeded(11)   12.9412% completed.    
succeeded(12)   14.1176% completed.    
succeeded(13)   15.2941% completed.    
succeeded(14)   16.4706% completed.    
succeeded(15)   17.6471% completed.    
succeeded(16)   18.8235% completed.    
succeeded(17)   20% completed.    
succeeded(18)   21.1765% completed.    
succeeded(19)   22.3529% completed.    
succeeded(20)   23.5294% completed.    
succeeded(21)   24.7059% completed.    
succeeded(22)   25.8824% completed.    
succeeded(23)   27.0588% completed.    
succeeded(24)   28.2353% completed.    
succeeded(25)   29.4118% completed.    
succeeded(26)   30.5882% completed.    
succeeded(27)   31.7647% completed.    
succeeded(28)   32.9412% completed.    
succeeded(29)   34.1176% completed.    
succeeded(30)   35.2941% completed.    
succeeded(31)   36.4706% completed.    
succeeded(32)   37.6471% completed.    
succeeded(33)   38.8235% completed.    
succeeded(34)   40% completed.    
succeeded(35)   41.1765% completed.    
succeeded(36)   42.3529% completed.    
succeeded(37)   43.5294% completed.    
succeeded(38)   44.7059% completed.    
succeeded(39)   45.8824% completed.    
succeeded(40)   47.0588% completed.    
succeeded(41)   48.2353% completed.    
succeeded(42)   49.4118% completed.    
succeeded(43)   50.5882% completed.    
succeeded(44)   51.7647% completed.    
succeeded(45)   52.9412% completed.    
succeeded(46)   54.1176% completed.    
succeeded(47)   55.2941% completed.    
succeeded(48)   56.4706% completed.    
succeeded(49)   57.6471% completed.    
succeeded(50)   58.8235% completed.    
succeeded(51)   60% completed.    
succeeded(52)   61.1765% completed.    
succeeded(53)   62.3529% completed.    
succeeded(54)   63.5294% completed.    
succeeded(55)   64.7059% completed.    
succeeded(56)   65.8824% completed.    
succeeded(57)   67.0588% completed.    
succeeded(58)   68.2353% completed.    
succeeded(59)   69.4118% completed.    
succeeded(60)   70.5882% completed.    
succeeded(61)   71.7647% completed.    
succeeded(62)   72.9412% completed.    
succeeded(63)   74.1176% completed.    
succeeded(64)   75.2941% completed.    
succeeded(65)   76.4706% completed.    
succeeded(66)   77.6471% completed.    
succeeded(67)   78.8235% completed.    
succeeded(68)   80% completed.    
succeeded(69)   81.1765% completed.    
succeeded(70)   82.3529% completed.    
succeeded(71)   83.5294% completed.    
succeeded(72)   84.7059% completed.    
succeeded(73)   85.8824% completed.    
succeeded(74)   87.0588% completed.    
succeeded(75)   88.2353% completed.    
succeeded(76)   89.4118% completed.    
succeeded(77)   90.5882% completed.    
succeeded(78)   91.7647% completed.    
succeeded(79)   92.9412% completed.    
succeeded(80)   94.1176% completed.    
succeeded(81)   95.2941% completed.    
succeeded(82)   96.4706% completed.    
succeeded(83)   97.6471% completed.    
succeeded(84)   98.8235% completed.    
succeeded(85)   100% completed.    
1902s 
1902s All commands completed successfully. :-)
1902s 
1902s Friday, November 1, 2024: 10:40:17	CMD: find Dir_*  -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta.tmp
1902s Friday, November 1, 2024: 10:40:17	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta.gene_trans_map
1902s 
1902s 
1902s Finished. See /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta for reconstructed transcripts
1902s 
1902s 
1902s 
1902s ok
1902s ./run_chr17_GG_wLongreads.sh
1902s outfile="test_GG_use_small_multiscaff_bam_trinity_outdir/Trinity-GG.fasta"
1902s asmsize=$(wc -c <"${outfile}")
1902s if [ $asmsize -le 650000 ]; then
1902s     echo "Error, ${outfile} potentially incomplete"
1902s     exit 1
1902s else
1902s     echo "ok"
1902s     exit 0
1902s fi
1902s #!/bin/bash -ve
1902s 
1902s 
1902s $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
1902s 
1902s 
1902s      ______  ____   ____  ____   ____  ______  __ __
1902s     |      ||    \ |    ||    \ |    ||      ||  |  |
1902s     |      ||  D  ) |  | |  _  | |  | |      ||  |  |
1902s     |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
1902s       |  |  |    \  |  | |  |  | |  |   |  |  |___, |
1902s       |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
1902s       |__|  |__|\_||____||__|__||____|  |__|  |____/
1902s 
1902s     Trinity-v2.15.1
1902s 
1902s 
1902s 
1902s Friday, November 1, 2024: 10:40:17	CMD: /usr/lib/trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl chr17.illumina.bam
1902s -appears to be a coordinate sorted bam file. ok.
1902s Friday, November 1, 2024: 10:40:17	CMD: mkdir -p /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir
1902s 
1902s 
1902s ----------------------------------------------------------------------------------
1902s -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
1902s ----------------------------------------------------------------------------------
1902s 
1902s -found paired-end aligned read. Running in paired-end mode.
1902s Friday, November 1, 2024: 10:40:17	CMD: /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/bamsifter -c 200 -o /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.illumina.bam
1903s Done with chr chr1.
1903s Friday, November 1, 2024: 10:40:18	CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.illumina.bam.norm_200.bam.ok
1903s * [Fri Nov  1 10:40:18 2024] Running CMD: java -jar /usr/share/java/picard.jar AddOrReplaceReadGroups I=/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam  O=/tmp/autopkgtest.xkSdGF/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
1905s INFO	2024-11-01 10:40:20	AddOrReplaceReadGroups	
1905s 
1905s ********** NOTE: Picard's command line syntax is changing.
1905s **********
1905s ********** For more information, please see:
1905s ********** 
1905s https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
1905s **********
1905s ********** The command line looks like this in the new syntax:
1905s **********
1905s **********    AddOrReplaceReadGroups -I /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam -O /tmp/autopkgtest.xkSdGF/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
1905s **********
1905s 
1905s 
1905s 10:40:20.484 WARN  NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
1905s 10:40:20.488 WARN  NativeLibraryLoader - LD_LIBRARY_PATH = :/usr/lib/trinityrnaseq/trinity-plugins/htslib
1905s 10:40:20.488 WARN  NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
1905s 10:40:20.491 WARN  NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
1905s 10:40:20.491 WARN  NativeLibraryLoader - LD_LIBRARY_PATH = :/usr/lib/trinityrnaseq/trinity-plugins/htslib
1905s 10:40:20.491 WARN  NativeLibraryLoader - OVERRIDE DEFAULT: Unable to load libgkl_compression.so from :/usr/lib/trinityrnaseq/trinity-plugins/htslib:/usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
1905s [Fri Nov 01 10:40:20 UTC 2024] AddOrReplaceReadGroups INPUT=/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam OUTPUT=/tmp/autopkgtest.xkSdGF/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
1905s [Fri Nov 01 10:40:20 UTC 2024] Executing as ubuntu@autopkgtest on Linux 6.11.0-8-generic aarch64; OpenJDK 64-Bit Server VM 21.0.5+11-Ubuntu-1; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: 3.1.1
1905s 10:40:20.517 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
1905s 10:40:20.524 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
1905s INFO	2024-11-01 10:40:20	AddOrReplaceReadGroups	Created read-group ID=PBLR PL=pacbio LB=lib2 SM=pacbio
1905s 
1905s 10:40:20.567 WARN  IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
1905s [Fri Nov 01 10:40:20 UTC 2024] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.01 minutes.
1905s Runtime.totalMemory()=67108864
1905s * [Fri Nov  1 10:40:20 2024] Running CMD: samtools merge /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.illumina.bam.norm_200.bam /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/chr17.pbio.bam.RGLR.bam && samtools index /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam
1906s Friday, November 1, 2024: 10:40:21	CMD: /usr/lib/trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /tmp/autopkgtest.xkSdGF/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 
1906s 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 
1906s -extracting read coordinates from merged_wRGLR.bam into merged_wRGLR.bam.read_coords
1906s 
1908s CMD: touch merged_wRGLR.bam.read_coords.ok
1908s 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
1908s CMD: cp /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam.read_coords /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/merged_wRGLR.bam.read_coords.sort_by_readname
1908s CMD: /usr/bin/sort --parallel=5 -S2G -T . -k1,1 -k3,3n merged_wRGLR.bam.frag_coords > merged_wRGLR.bam.frag_coords.coord_sorted
1909s CMD: /usr/lib/trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl merged_wRGLR.bam.frag_coords > merged_wRGLR.bam.frag_coverage.wig
1925s 
[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
1925s CMD: /usr/lib/trinityrnaseq/util/support_scripts/define_coverage_partitions.pl merged_wRGLR.bam.frag_coverage.wig 1 + > merged_wRGLR.bam.minC1.gff
1929s CMD: touch merged_wRGLR.bam.minC1.gff.ok
1929s 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 
1929s // parsing paritions.
1929s 
[100]  
[116]  -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/60324_60754.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/60950_61267.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/61474_118580.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/205351_205672.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/210418_210982.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/213769_219690.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/229120_229684.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/263847_264260.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/270652_271297.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/281768_441038.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/441045_445940.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/511494_511801.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/512042_512389.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/512759_514091.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/514571_714865.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/714910_715353.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/715370_716236.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/716302_716978.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/717455_718543.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/718787_719490.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/719569_720181.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/720720_721596.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/721666_722031.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/726239_726536.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/729712_730684.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/730918_731668.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/731742_732126.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/732418_752287.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/752375_752769.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/753167_754706.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/758974_782331.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/782362_792510.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/793543_794109.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/795176_795754.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/799707_800316.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/800915_803792.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/981902_982655.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/997125_1091796.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1146722_1146846.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1148302_1149226.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1151011_1152011.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1153293_1153810.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1226770_1227467.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1257967_1400270.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1414443_1415081.trinity.reads
1929s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/1420724_2022954.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2030147_2043980.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2044654_2045225.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2047917_2048512.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2049091_2049553.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2051694_2052378.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2053479_2053635.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2054237_2054372.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2054544_2056751.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2056812_2057391.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2058177_2058912.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2059847_2303836.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2303955_2336468.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2336627_2337019.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2337198_2381047.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2384152_2401123.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2401365_2401725.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2404365_2404707.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2405573_2732999.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2956146_2956563.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2975679_2985002.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/2991366_3008124.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3020537_3033568.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3033777_3034364.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3035321_3035959.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3036150_3036658.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3267590_3274822.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3328495_3331689.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3421757_3422307.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3422776_3423370.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3440227_3513828.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3565576_3566168.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3566800_3572235.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3573782_3585901.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3586814_3587176.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3589817_3592166.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3592533_3592851.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3605115_3605237.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3606109_3607928.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3607968_3636272.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3636486_3668698.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3668798_3670060.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3670078_3670807.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3673537_3681945.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3689987_3695886.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3706252_3917856.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3923874_3964467.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/3964821_3965192.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4001444_4001952.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4003050_4003706.trinity.reads
1930s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4004424_4555389.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4660854_4661151.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4667839_4668289.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4671192_4704136.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/0/4704234_4705420.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4710502_4721496.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4731419_4733592.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4734646_4739376.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4787354_4789638.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4796155_4798495.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4805950_4806545.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4807192_4823373.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4833366_4897982.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4904417_4904897.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4927248_4928577.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4928729_4928949.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4929025_4934979.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4935086_4935300.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4935439_4945214.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4945652_4997520.trinity.reads
1931s -writing to Dir_merged_wRGLR.bam.minC1.gff/chr17/1/4997681_5001302.trinity.reads
1931s CMD: touch Dir_merged_wRGLR.bam.minC1.gff.ok
1931s ##
1931s Done
1931s ##
1931s 
1931s Friday, November 1, 2024: 10:40:46	CMD: touch partitions.ok
1931s Friday, November 1, 2024: 10:40:46	CMD: find Dir_* -name '*reads' > read_files.list
1931s Friday, November 1, 2024: 10:40:46	CMD: touch read_files.list.ok
1931s Friday, November 1, 2024: 10:40:46	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
1931s Friday, November 1, 2024: 10:40:46	CMD: touch trinity_GG.cmds.ok
1931s Friday, November 1, 2024: 10:40:46	CMD: touch trinity_GG.cmds.ok
1931s 
1931s 
1931s --------------------------------------------------------------------------------
1931s ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
1931s ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
1931s --------------------------------------------------------------------------------
1931s 
1931s Friday, November 1, 2024: 10:40:46	CMD: /usr/bin/ParaFly -c trinity_GG.cmds -CPU 5 -v -shuffle 
1931s Number of Commands: 44
2856s 
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.    
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2856s 
2856s All commands completed successfully. :-)
2856s 
2856s Friday, November 1, 2024: 10:56:11	CMD: find Dir_*  -name '*inity.fasta'  | /usr/lib/trinityrnaseq/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta.tmp
2856s Friday, November 1, 2024: 10:56:11	CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta.gene_trans_map
2856s 
2856s 
2856s Finished. See /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/test_chr17_LR_GG_trinity_outdir/Trinity-GG.fasta for reconstructed transcripts
2856s 
2856s 
2856s find test_chr17_LR_GG_trinity_outdir/ -regex ".*allProbPaths.fasta" -exec cat {} \; | grep '>' | grep 'LR\$' > test_chr17_LR_GG_trinity_outdir.LR
2857s touch test
2857s 
2857s if [[ $(wc -l <test_chr17_LR_GG_trinity_outdir.LR) -le 200 ]]; then
2857s     echo "Error, fewer than expected pbio read-integrated assembled transcripts"
2857s     exit 1
2857s fi
2857s 
2857s 
2857s exit 0
2857s make[1]: Leaving directory '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity'
2857s Running example in test_InSilicoReadNormalization...
2857s make[1]: Entering directory '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization'
2857s ./test_PE_normalization.sh
2857s #!/bin/bash -ve
2857s 
2857s CPU=$(nproc || sysctl -n hw.physicalcpu)
2857s 
2857s # just for testing purposes, use --max_cov 30 or higher for real applications.
2857s $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
2857s -prepping seqs
2857s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz) >> left.fa
2857s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz) >> right.fa
2858s CMD finished (1 seconds)
2858s CMD finished (1 seconds)
2858s CMD: touch left.fa.ok
2858s CMD finished (0 seconds)
2858s CMD: touch right.fa.ok
2858s CMD finished (0 seconds)
2858s Done converting input files.CMD: cat left.fa right.fa > both.fa
2858s CMD finished (0 seconds)
2858s CMD: touch both.fa.ok
2858s CMD finished (0 seconds)
2858s -kmer counting.
2858s -------------------------------------------
2858s ----------- Jellyfish  --------------------
2858s -- (building a k-mer catalog from reads) --
2858s -------------------------------------------
2858s 
2858s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  both.fa
2859s CMD finished (1 seconds)
2859s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
2859s CMD finished (0 seconds)
2859s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
2859s CMD finished (0 seconds)
2859s CMD: touch jellyfish.K25.min2.kmers.fa.success
2859s CMD finished (0 seconds)
2859s -generating stats files
2859s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > left.fa.K25.stats
2859s -reading Kmer occurrences...
2859s 
2859s  done parsing 100964 Kmers, 100964 added, taking 0 seconds.
2859s STATS_GENERATION_TIME: 0 seconds.
2859s CMD finished (0 seconds)
2859s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > right.fa.K25.stats
2859s -reading Kmer occurrences...
2860s 
2860s  done parsing 100964 Kmers, 100964 added, taking 0 seconds.
2860s STATS_GENERATION_TIME: 1 seconds.
2860s CMD finished (1 seconds)
2860s CMD: touch left.fa.K25.stats.ok
2860s CMD finished (0 seconds)
2860s CMD: touch right.fa.K25.stats.ok
2860s CMD finished (0 seconds)
2860s -sorting each stats file by read name.
2860s 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
2860s CMD finished (0 seconds)
2860s 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
2860s CMD finished (0 seconds)
2860s CMD: touch left.fa.K25.stats.sort.ok
2860s CMD finished (0 seconds)
2860s CMD: touch right.fa.K25.stats.sort.ok
2860s CMD finished (0 seconds)
2860s -defining normalized reads
2860s 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
2860s -opening left.fa.K25.stats.sort
2860s -opening right.fa.K25.stats.sort
2860s -done opening files.
2860s CMD finished (0 seconds)
2860s CMD: touch pairs.K25.stats.ok
2860s CMD finished (0 seconds)
2860s 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
2861s 3826 / 30575 = 12.51% reads selected during normalization.
2861s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
2861s 1797 / 30575 = 5.88% reads discarded as below minimum coverage threshold=2
2861s CMD finished (1 seconds)
2861s CMD: touch pairs.K25.stats.C5.maxCV10000.accs.ok
2861s CMD finished (0 seconds)
2861s -search and capture.
2861s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz ... done prepping, now search and capture.
2861s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz
2861s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz ... done prepping, now search and capture.
2861s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz
2861s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.left.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq.ok
2861s CMD finished (0 seconds)
2861s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.right.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq.ok
2861s CMD finished (0 seconds)
2861s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.left.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq left.norm.fq
2861s CMD finished (0 seconds)
2861s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.right.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq right.norm.fq
2861s CMD finished (0 seconds)
2861s 
2861s 
2861s Normalization complete. See outputs: 
2861s 	/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.left.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq
2861s 	/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.right.fq.gz.normalized_K25_maxC5_minC2_maxCV10000.fq
2861s ./test_SE_normalization.sh
2861s 
2861s 
2861s 
2861s #!/bin/bash -ve
2861s 
2861s if [ ! -e reads.single.fq ]; then
2861s     gunzip -c ../test_DATA/reads.left.fq.gz > reads.single.fq
2861s fi
2861s 
2861s 
2861s # just for testing purposes, use --max_cov 30 or higher for real applications.
2861s $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
2861s -prepping seqs
2861s CMD: seqtk-trinity seq -A -R 1  /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq >> single.fa
2861s CMD finished (0 seconds)
2861s CMD: touch single.fa.ok
2861s CMD finished (0 seconds)
2861s -kmer counting.
2861s -------------------------------------------
2861s ----------- Jellyfish  --------------------
2861s -- (building a k-mer catalog from reads) --
2861s -------------------------------------------
2861s 
2861s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  single.fa
2862s CMD finished (1 seconds)
2862s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
2862s CMD finished (0 seconds)
2862s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
2862s CMD finished (0 seconds)
2862s CMD: touch jellyfish.K25.min2.kmers.fa.success
2862s CMD finished (0 seconds)
2862s -generating stats files
2862s CMD: /usr/bin/fastaToKmerCoverageStats --reads single.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > single.fa.K25.stats
2862s -reading Kmer occurrences...
2862s 
2862s  done parsing 70076 Kmers, 70076 added, taking 0 seconds.
2863s STATS_GENERATION_TIME: 1 seconds.
2863s CMD finished (1 seconds)
2863s CMD: touch single.fa.K25.stats.ok
2863s CMD finished (0 seconds)
2863s -sorting each stats file by read name.
2863s 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
2863s CMD finished (0 seconds)
2863s CMD: touch single.fa.K25.stats.sort.ok
2863s CMD finished (0 seconds)
2863s -defining normalized reads
2863s 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
2863s 9127 / 30575 = 29.85% reads selected during normalization.
2863s 0 / 30575 = 0.00% reads discarded as likely aberrant based on coverage profiles.
2863s 0 / 30575 = 0.00% reads discarded as below minimum coverage threshold=0
2863s CMD finished (0 seconds)
2863s CMD: touch single.fa.K25.stats.sort.maxC5.minC0.maxCV10000.accs.ok
2863s CMD finished (0 seconds)
2863s -search and capture.
2863s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq ... done prepping, now search and capture.
2863s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq
2863s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq.normalized_K25_maxC5_minC0_maxCV10000.fq.ok
2863s CMD finished (0 seconds)
2863s CMD: ln -sf /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq.normalized_K25_maxC5_minC0_maxCV10000.fq single.norm.fq
2863s CMD finished (0 seconds)
2863s 
2863s 
2863s Normalization complete. See outputs: 
2863s 	/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/reads.single.fq.normalized_K25_maxC5_minC0_maxCV10000.fq
2863s ./test_PE_normalization.mult_read_sets.sh
2863s 
2863s 
2863s 
2863s #!/bin/bash -ve
2863s 
2863s CPU=$(nproc || sysctl -n hw.physicalcpu)
2863s 
2863s # just for testing purposes, use --max_cov 30 or higher for real applications.
2863s $TRINITY_HOME/util/insilico_read_normalization.pl --JM 2G \
2863s      --left ../test_DATA/reads.left.fq.gz,../test_DATA/reads2.left.fq.gz \
2863s      --right ../test_DATA/reads.right.fq.gz,../test_DATA/reads2.right.fq.gz \
2863s      --seqType fq --max_cov 5 --pairs_together --no_cleanup --CPU ${CPU} --tmp_dir_name tmp_PE_mult_norm_dir \
2863s      --output test_multi_read_sets_norm_outdir
2863s -prepping seqs
2863s Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz) >> left.fa
2863s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz) >> right.fa
2863s CMD finished (0 seconds)
2863s CMD: seqtk-trinity seq -A -R 1  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.left.fq.gz) >> left.fa
2863s CMD finished (0 seconds)
2863s CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.right.fq.gz) >> right.fa
2864s CMD finished (1 seconds)
2864s CMD finished (1 seconds)
2864s CMD: touch left.fa.ok
2864s CMD finished (0 seconds)
2864s CMD: touch right.fa.ok
2864s CMD finished (0 seconds)
2864s Done converting input files.CMD: cat left.fa right.fa > both.fa
2864s CMD finished (0 seconds)
2864s CMD: touch both.fa.ok
2864s CMD finished (0 seconds)
2864s -kmer counting.
2864s -------------------------------------------
2864s ----------- Jellyfish  --------------------
2864s -- (building a k-mer catalog from reads) --
2864s -------------------------------------------
2864s 
2864s CMD: jellyfish count -t 2 -m 25 -s 100000000  --canonical  both.fa
2865s CMD finished (1 seconds)
2865s CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
2865s CMD finished (0 seconds)
2865s CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
2865s CMD finished (0 seconds)
2865s CMD: touch jellyfish.K25.min2.kmers.fa.success
2865s CMD finished (0 seconds)
2865s -generating stats files
2865s CMD: /usr/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > left.fa.K25.stats
2865s -reading Kmer occurrences...
2866s 
2866s  done parsing 518514 Kmers, 518514 added, taking 1 seconds.
2867s STATS_GENERATION_TIME: 1 seconds.
2867s CMD finished (2 seconds)
2867s CMD: /usr/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > right.fa.K25.stats
2867s -reading Kmer occurrences...
2867s 
2867s  done parsing 518514 Kmers, 518514 added, taking 0 seconds.
2868s STATS_GENERATION_TIME: 1 seconds.
2868s CMD finished (1 seconds)
2868s CMD: touch left.fa.K25.stats.ok
2868s CMD finished (0 seconds)
2868s CMD: touch right.fa.K25.stats.ok
2868s CMD finished (0 seconds)
2868s -sorting each stats file by read name.
2868s 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
2868s CMD finished (0 seconds)
2868s 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
2868s CMD finished (0 seconds)
2868s CMD: touch left.fa.K25.stats.sort.ok
2868s CMD finished (0 seconds)
2868s CMD: touch right.fa.K25.stats.sort.ok
2868s CMD finished (0 seconds)
2868s -defining normalized reads
2868s 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
2868s -opening left.fa.K25.stats.sort
2868s -opening right.fa.K25.stats.sort
2868s -done opening files.
2869s CMD finished (1 seconds)
2869s CMD: touch pairs.K25.stats.ok
2869s CMD finished (0 seconds)
2869s 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
2870s 7970 / 61150 = 13.03% reads selected during normalization.
2870s 0 / 61150 = 0.00% reads discarded as likely aberrant based on coverage profiles.
2870s 0 / 61150 = 0.00% reads discarded as below minimum coverage threshold=0
2870s CMD finished (1 seconds)
2870s CMD: touch pairs.K25.stats.C5.maxCV10000.accs.ok
2870s CMD finished (0 seconds)
2870s -search and capture.
2870s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.left.fq.gz ... done prepping, now search and capture.
2870s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.left.fq.gz
2870s -preparing to extract selected reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.right.fq.gz ... done prepping, now search and capture.
2870s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads.right.fq.gz
2870s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.right.fq.gz
2870s -capturing normalized reads from: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/../test_DATA/reads2.left.fq.gz
2870s CMD: touch /tmp/autopkgtest.xkSdGF/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
2870s CMD finished (0 seconds)
2870s CMD: touch /tmp/autopkgtest.xkSdGF/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
2870s CMD finished (0 seconds)
2870s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
2870s CMD finished (0 seconds)
2870s CMD: ln -sf /tmp/autopkgtest.xkSdGF/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
2870s CMD finished (0 seconds)
2870s 
2870s 
2870s Normalization complete. See outputs: 
2870s 	/tmp/autopkgtest.xkSdGF/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
2870s 	/tmp/autopkgtest.xkSdGF/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
2870s 
2870s 
2870s 
2870s touch test
2870s make[1]: Leaving directory '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization'
2870s Running example in test_DE_analysis...
2870s make[1]: Entering directory '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis'
2870s Running example in Candida_example...
2870s make[2]: Entering directory '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example'
2870s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_DE_analysis.pl  -m Trinity_trans.counts.matrix --method edgeR -s samples.txt -o edgeR_outdir
2870s Got 9 samples, and got: 10 data fields.
2870s 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
2870s Next: TR24|c0_g1_i1	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
2870s 
2870s $VAR1 = {
2870s           'wt_37_3' => 2,
2870s           'wt_ph8_3' => 7,
2870s           'wt_37_1' => 3,
2870s           'wt_GSNO_3' => 4,
2870s           'wt_ph8_2' => 9,
2870s           'wt_37_2' => 1,
2870s           'wt_GSNO_1' => 5,
2870s           'wt_ph8_1' => 8,
2870s           'wt_GSNO_2' => 6
2870s         };
2870s $VAR1 = {
2870s           'wt_GSNO' => [
2870s                          'wt_GSNO_1',
2870s                          'wt_GSNO_2',
2870s                          'wt_GSNO_3'
2870s                        ],
2870s           'wt_ph8' => [
2870s                         'wt_ph8_1',
2870s                         'wt_ph8_2',
2870s                         'wt_ph8_3'
2870s                       ],
2870s           'wt_37' => [
2870s                        'wt_37_1',
2870s                        'wt_37_2',
2870s                        'wt_37_3'
2870s                      ]
2870s         };
2870s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.wt_37.vs.wt_GSNO.EdgeR.Rscript
2870s Contrasts to perform are: $VAR1 = [
2870s           [
2870s             'wt_37',
2870s             'wt_GSNO'
2870s           ],
2870s           [
2870s             'wt_37',
2870s             'wt_ph8'
2870s           ],
2870s           [
2870s             'wt_GSNO',
2870s             'wt_ph8'
2870s           ]
2870s         ];
2871s Loading required package: edgeR
2871s Loading required package: limma
2871s Using classic mode.
2873s null device 
2873s           1 
2873s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.wt_37.vs.wt_ph8.EdgeR.Rscript
2873s Loading required package: edgeR
2873s Loading required package: limma
2874s Using classic mode.
2876s null device 
2876s           1 
2876s CMD: Rscript Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.wt_GSNO.vs.wt_ph8.EdgeR.Rscript
2876s Loading required package: edgeR
2876s Loading required package: limma
2876s Using classic mode.
2878s null device 
2878s           1 
2878s cd edgeR_outdir && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl  \
2878s --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt && \
2878s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt
2878s 
2878s 
2878s ** Found 2062 features as differentially expressed.
2878s 
2878s 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
2879s CMD: Rscript diffExpr.P0.001_C2.matrix.R
2879s Loading required package: BiocGenerics
2879s 
2879s Attaching package: ‘BiocGenerics’
2879s 
2879s The following objects are masked from ‘package:stats’:
2879s 
2879s     IQR, mad, sd, var, xtabs
2879s 
2879s The following objects are masked from ‘package:base’:
2879s 
2879s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2879s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2879s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2879s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2879s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
2879s     tapply, union, unique, unsplit, which.max, which.min
2879s 
2879s Welcome to Bioconductor
2879s 
2879s     Vignettes contain introductory material; view with
2879s     'browseVignettes()'. To cite Bioconductor, see
2879s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2879s 
2880s [1] "Reading matrix file."
2880s 
2880s Attaching package: ‘fastcluster’
2880s 
2880s The following object is masked from ‘package:stats’:
2880s 
2880s     hclust
2880s 
2881s for plotting:: min.raw: -0.643115788375154 max.raw: 1
2881s null device 
2881s           1 
2882s for plotting:: min.raw: -7.50284849776958 max.raw: 7.50284849776958
2882s null device 
2882s           1 
2883s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_37-UP.subset 
2883s 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 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_37-UP.subset) passes test.
2883s 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 
2883s 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 
2883s num discordant:  0 
2883s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset 
2883s 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 
2883s sampleB_mean:  381.073 324.8553 363.4697 136.0917 1076.978 135.6287 721.2523 193.995 322.6313 501.0717 7779.492 155.6753 2550.414 340.8923 1492.051 9939.373 303.273 1007.03 1438.471 1331.648 7520.41 6944.853 217.5877 6464.644 973.0083 7181.47 971.4367 2449.757 2827.345 11165.49 5346.478 10849.9 2510.784 3982.392 347.4017 722.7793 440.9727 204.688 188.059 227.1767 183.432 341.9023 304.1167 1192.947 1506.715 318.3057 1781.496 147.2877 6705.697 644.756 98.27667 8614.152 8614.152 6887.084 636.1717 510.9113 876.8277 819.1427 5036.385 568.9407 293.4293 512.042 4540.328 5874.642 6156.043 5974.238 176.1237 88.77667 381.4813 850.5097 204.598 132.997 5515.698 224.959 7405.14 297.5633 820.1 3398.294 803.7297 493.2167 337.5617 2649.173 374.99 728.6047 1237.565 3104.744 347.1993 7596.105 568.3683 91.93733 4809.412 286.7303 5589.41 8313.711 464.25 395.6523 3325.992 4978.607 199.5333 210.5073 615.4837 190.3363 237.9167 234.8707 327.728 8625.824 8726.054 1183.775 4624.974 254.0923 165.5147 177.6103 592.331 229.8227 307.597 498.566 12136.75 4181.758 126.265 3101.543 257.8713 318.668 437.8937 11956.17 2806.072 209.5997 880.4753 124.821 96.888 330.2803 178.331 265.4807 565.0517 10695.83 59.968 107.6607 133.1137 5311.835 497.3057 369.4417 9160.812 65.022 189.81 361.7567 66.28233 240.9067 79.23 148.3807 92.04867 277.6277 1388.008 1147.187 744.834 617.5097 10005.84 3135.76 624.4283 177.0987 437.7077 169.5693 501.203 130.7987 163.2497 365.9053 3477.406 5150.462 464.656 85.369 2813.865 227.959 396.4167 159.9217 248.7967 7921.826 1232.959 87.30767 139.8577 4052.112 58.786 223.6213 303.588 784.5 12803.12 201.1477 309.0137 129.359 205.964 151.089 3606.195 8077.68 7646.521 365.304 366.6233 2069.238 242.2357 196.2657 102.4913 198.0453 171.415 221.5063 9231.562 146.225 53.11833 76.629 198.031 11807.78 7137.863 346.0203 14596.83 141.1233 244.213 94.084 221.3943 3043.903 1727.754 228.616 115.6383 954.507 134.7863 186.3673 3497.592 343.3797 171.2443 160.6447 118.4783 176.1103 794.7277 41.92667 79.78767 374.3023 2899.79 383.3883 132.86 243.0527 434.0653 332.1927 204.0893 383.105 306.1523 259.974 56.084 153.6373 102.4957 160.461 566.3103 473.468 5955.872 138.7943 297.5293 1314.765 93.961 165.6487 92.801 88.20067 5402.498 175.727 376.801 1374.415 208.997 324.095 38.50333 219.043 578.1793 261.1813 166.719 7998.991 145.871 146.7367 109.0163 88.84733 106.9733 112.8707 7391.381 55.56067 217.828 58.52433 2636.168 92.66933 82.77467 110.12 199.25 65.82467 10466.26 84.19433 317.4007 1924.887 506.512 434.5497 162.353 434.0367 264.5573 241.8647 51.48067 4659.391 279.8187 12057.81 79.15267 104.7473 210.276 108.0163 44.52667 130.4647 2478.864 219.1713 1538.062 60.909 120.016 502.0593 125.9207 54.28 102.9103 404.8233 102.8277 189.876 59.07767 288.2643 109.1297 67.97633 1485.8 92.14267 138.9953 71.07333 65.14433 221.9553 42.94067 155.6507 63.51467 94.855 205.7273 49.84633 451.6893 139.4217 91.36867 72.27033 88.724 53.67933 136.3853 91.96267 251.6407 446.5917 101.2043 142.4997 147.5143 150.83 64.48933 125.6427 2983.166 98.42267 31019.62 72.04033 391.7213 217.945 244.312 114.7247 313.5353 1573.052 188.654 92.354 1190.783 54.17467 98.59367 78.15767 138.8203 94.036 57.92467 72.229 3680.324 57.289 71.95633 329.0943 48.662 284.8557 359.4497 117.3687 147.9097 112.4907 89.19033 160.033 80.658 323.135 272.869 177.7223 205.2823 6554.638 75.13167 143.6177 67.32633 92.10033 55.31033 111.3283 92.91767 71.83833 92.673 58.84033 123.7103 83.32767 68.93667 64.96333 97.74133 33.64933 66.58633 63.519 86.666 61.75633 114.413 126.6667 61.049 52.40167 62.202 70.82967 31.92033 558.288 54.697 97.67333 98.25867 189.338 1437.071 86.82867 55.42833 51.40267 185.3687 26.105 1768.526 143.2053 69.31567 27.42533 36.84367 23095.85 654.0063 106.367 92.58367 84.09433 63.39167 29.412 65.265 25.16133 49.55567 23.09333 59.70833 30.305 61.927 60.39433 12433.72 44.59133 91.34767 108.9977 629.935 47.69867 37.13833 80.30267 59.309 38.35733 21.31667 36.129 40.01867 97.91867 56.87433 100.9357 74.47967 101.2333 40.88467 41.25767 29.19933 44.65167 75.314 81.03933 67.40867 63.275 52.62167 70.48667 28.11233 89.473 20.836 65.641 18.746 57.89033 36.83567 63.43233 39.14833 51.208 50.94033 37.861 105.9517 33.71767 82.208 269.8203 37.373 59.017 45.43467 180.145 46.01667 53.35367 51.20733 72.092 38.239 17.67167 58.72433 70.23367 118.5717 36.76167 40.58467 43.553 48.09067 104.9537 32.39167 95.03067 31.81733 74.76 24.105 42.02167 63.80367 40.14133 44.57067 16.39933 134.3513 17.20333 57.38933 44.80233 52.59533 71.77333 37.18267 49.809 60.34067 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test.
2883s 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 
2883s num discordant:  0 
2883s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_37-UP.subset 
2883s 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 
2883s sampleB_mean:  4.892333 0.8923333 3.02 10.731 1.413333 4.947333 4.916 2.201 5.897667 1.439333 11.541 126.2827 5.31 5.982333 18.24467 28.83167 71.58533 15.897 11.73133 54.76233 7.353333 9.523667 20.785 20.73967 10.32667 34.85667 21.734 39.02467 18.007 15.272 14.071 67.15133 190.2367 11.974 175.0553 46.38933 162.736 38.35033 40.62 61.93367 231.01 644.6073 17.87533 149.0183 38.834 1576.856 120.2997 60.698 70.315 84.69133 10.01733 5.055333 122.321 6.593 176.7203 5.075 6.833333 143.0547 34.29367 312.258 4.303333 20.43633 62.01667 6.119333 52.632 2.999 41.809 18.10167 44.774 82.944 191.4833 21.86767 17.35367 131.954 97.40133 184.242 33.76633 11.08667 31.756 216.263 91.85267 51.789 69.84367 85.388 21.75133 167.6013 68.43533 46.20633 70.838 10.803 199.414 78.63867 1058.536 18.98533 34.63 5.957333 6.52 8.328333 146.7283 32.09667 13.45833 154.1127 8.807333 29.81633 18.10667 94.25133 327.4777 3.039667 14.93967 172.0003 19.323 62.69867 10.14033 167.5307 1.982 107.587 120.642 99.03833 5.291 13.40767 176.0093 48.44967 1.620333 9.162667 52.029 7.044667 86.94433 96.643 17.25433 290.869 59.39767 44.574 22.66633 60.149 138.9923 5.435 33.99767 81.38067 29.81667 57.83967 35.93933 18.47767 263.582 24.10267 157.5777 151.9077 274.274 3.384 147.5103 135.326 296.326 119.8197 585.796 5.086333 7.705667 98.93967 138.5447 45.153 12.202 111.2203 78.18267 236.2837 81.65333 3.080667 52.72333 288.293 60.40333 112.516 9.454333 29.03533 11.36967 71.425 11.83333 11.37767 36.04767 62.152 25.95767 81.69867 10.11133 31.115 40.80033 16.697 33.16933 31.26267 15.18533 68.39567 4.436 37.04267 33.04933 15.958 52.859 22.379 4.922 77.499 77.462 239.1367 228.12 31.045 131.7207 64.78833 76.85 22.86333 14.63133 46.24133 52.96867 29.20433 252.1407 44.73367 26.55867 43.10367 9.876 32.20767 46.83533 6.152333 42.20867 64.61967 21.17867 41.19767 41.53733 12.78767 11.56533 66.14267 2.519 19.13967 3.457 0.388 20.32033 28.43733 14.93967 12.457 192.615 81.672 80.735 55.72533 27.23467 68.06833 33.53433 24.19267 252.5313 60.023 3.929667 21.33367 11.13 22.53 13.001 27.607 37.84833 50.52767 15.63733 49.06433 21.97267 262.4237 28.67333 25.094 103.8797 92.249 24.55133 77.08667 9.053333 53.45667 57.499 221.51 129.8027 29.328 41.26233 16.52467 10.47367 38.40433 16.72967 36.59667 12.56167 17.05033 8.892333 16.70467 72.445 15.72 23.92933 4.478333 14.59467 15.84233 7.813 26.382 19.338 16.686 456.8783 3.546 72.39567 300.8857 58.95767 3.424 10.048 41.21667 6.782 26.43 161.046 49.04333 6.808667 38.81867 9.581333 10.136 20.181 15.967 2.343667 9.956333 10.61567 15.178 30.64367 11.71167 6.818 3.776 79.67267 2.932 19.69133 7.134 63.54133 603.3247 131.0337 10.08733 14.317 47.94933 12.49533 2.596 41.753 22.72933 144.8737 13.70767 9.795333 0 6.163 11.88467 5.698 9.696333 4.551667 6.056667 3.111 0.77 24.952 9.568 2.558333 8.861667 8.024 6.153 44.787 3.721 0.8253333 9.442 6.028 6.225333 15.87967 9.684333 7.286 5.855333 25.736 5.053 5.482333 5.451 5.704667 5.819667 9.387667 23.79767 8.245667 12.136 10.034 6.709 9.898 11.101 3.947333 13.348 6.474667 25.345 96.05 1.601 0 2.289 3.487 9.86 30.05333 15.06367 1.628667 10.75867 5.932 5.672667 4.229333 9.460667 0 10.76167 2.356667 1.994333 4.762667 0 34.28533 2.515333 2.445 6.930333 6.886 2.312667 6.758333 60.65633 12.28333 4.818333 2.695333 16.034 2.932333 3.923 4.023 4.175333 3.518 1.379333 18.601 3.183333 8.966667 4.880333 5.966667 5.916667 0 0.597 1.362 26.49267 8.657333 0 5.907333 2.795333 2.091333 0.3683333 3.392 2.201333 2.298667 1.082 0 1.805 5.972667 6.506333 10.182 3.766667 3.583333 4.613333 4.885 7.344667 0 4.728667 0.911 4.943333 2.479333 0 2.582 1.481667 7.661333 47.94667 2.759333 0 5.132 3.599 1.101667 2.819 3.284667 4.356 0.774 0.3263333 0 4.525 3.673667 1.016667 0.7583333 2.833333 8.528 7.471 0 1.173667 5.924 1.954333 2.414 2.116667 2.037 0 0 3.214 2.062 2.585333 2.919667 3.048 7.372333 3.673333 7.599 0.05333333 7.766333 3.431333 2.400667 16.083 3.17 0 4.567333 3.38 2.839333 4.954667 9.191667 3.975 5.980333 4.509333 3.139667 16.31167 1.766333 2.267 2.893333 4.752333 0 6.575 1.525 0 0.969 3.08 8.722 2.136333 7.809 1.796333 0 3.779333 1.799 2.693333 2.451 0.7883333 4.770333 1.826 4.1 0.831 
2883s num discordant:  0 
2883s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset 
2883s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_37-UP.subset) passes test.
2883s 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 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
2883s 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 
2883s 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 
2883s num discordant:  0 
2883s validating:  Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset 
2883s 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 
2883s 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 File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test.
2883s 51.37267 107.8423 84.69133 143.015 42.12067 162.736 98.93967 33.19 77.04167 149.042 72.11933 173.185 21.17867 107.4767 40.211 60.698 24.36067 11.974 3.97 231.01 230.7603 60.63 62.01667 361.5717 3.203 644.6073 91.85267 63.14733 147.5103 31.336 190.2367 149.0183 52.02367 8.328333 50.806 126.507 47.04433 22.66633 35.05467 5.375333 52.632 20.43633 14.771 4.436 15.897 21.67633 126.2827 21.66667 14.72967 22.414 23.35133 43.86567 30.432 27.23467 25.96333 3.546 61.038 113.391 52.72333 49.04333 13.34567 11.42567 5.980333 43.19967 35.93933 36.80733 4.816667 5.957333 38.81867 7.705667 6.593 603.3247 34.63 15.84233 15.47833 21.97267 84.23433 21.75133 11.08667 20.231 15.958 47.94933 13.23833 126.723 1.620333 11.73133 3.929667 6.119333 6.474667 24.79367 7.766333 5.855333 15.00967 21.74967 7.976 14.15433 7.353333 2.201333 7.205333 15.63733 21.066 0.6883333 4.916 101.151 0 1.439333 22.53 6.552 1.932 6.709 4.875667 21.36367 8.861667 2.48 4.478333 3.745333 10.64267 15.06367 0 3.039667 53.09067 7.033333 0 7.920333 2.116667 34.28533 3.831 3.374 6.818 14.63867 1.628667 12.223 3.003333 7.897667 5.966667 1.101667 0 5.451 6.937333 21.018 4.024 4.954667 8.839667 6.506333 6.301667 19.603 3.384 1.799 1.569 3.431333 14.62267 5.157 6.500333 8.477667 8.693333 1.63 1.082 14.45 10.157 5.139 1.765 8.006333 2.462333 3.485333 2.819 6.082333 2.909667 0.4836667 10.28 0.692 5.055333 0.08 0.05333333 7.749 10.15367 5.873 2.511 41.35533 9.145 2.893333 1.487333 5.417 13.05267 7.386333 19.24567 9.771667 4.422333 6.758333 0.8023333 2.849667 8.017333 12.1 2.936333 4.993333 2.181667 2.193667 5.261333 0 25.41533 5.657333 2.136333 4.229333 2.217667 4.762667 10.16333 16.907 1.362 4.943333 3.54 4.677 3.098 4.158333 9.295333 14.763 2.343667 10.456 8.646 12.014 0 1.481667 0 3.833667 0.8846667 6.111 2.732667 3.947333 2.95 6.918667 5.704667 2.289 4.627333 1.766333 6.405333 5.972667 2.344 3.367 3.727667 3.412667 3.223333 8.528 2.445 2.058 2.001 16.79133 1.764667 5.310333 5.351 10.56633 31.983 2.097 8.735 0 3.839 1.942 4.567333 7.471 16.31167 3.862 1.925667 0 2.384 7.252 5.472667 3.237667 0.911 2.312667 4.294667 0 0 2.121667 0 1.519333 8.592 2.345 2.112667 2.622333 1.783333 3.487 0 3.301 1.833667 4.401 2.345 0 1.633667 1.173667 0 0 0.3683333 3.405667 3.381 4.706333 6.860333 1.718 10.319 
2883s num discordant:  0 
2883s validating:  Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset 
2883s sampleA_mean:  4.98 16.50567 117.2063 112.322 62.58133 37.23367 40.96933 28.62567 210.276 110.7323 73.97767 77.55333 94.08633 56.147 95.99433 311.829 220.5287 24.33867 534.2237 138.353 191.8153 105.9497 53.11833 658.8357 135.901 407.2907 1020.23 773.7893 825.1763 59.968 124.4243 55.75367 501.0717 2661.226 0 65.965 30.499 81.05967 36.99433 53.687 88.495 36.84367 50.429 189.9813 132.8633 62.68467 21.54267 12.544 2.172 83.305 12.42267 180.8457 53.33433 17.029 341.9023 58.24233 14.554 25.096 104.7537 48.72833 42.797 47.89667 57.313 3.969667 49.103 193.8337 9.165333 3.122 17.875 39.58367 68.49367 17.60767 15.418 54.28 115.6623 6.042667 56.695 9.605 24.273 16.69733 21.25867 42.71533 19.86033 39.777 133.0233 336.3973 30.00467 35.78433 7.538 11.277 23.53367 41.80933 15.26033 199.8083 5.607667 16.22733 7.374 22.84267 8.516333 63.41767 21.14433 342.208 41.83033 40.53433 3.966667 10.63267 24.02367 103.5143 20.959 31.04633 25.39133 32.75133 41.856 23.71433 14.411 35.43333 5.832 57.13467 24.38833 14.56933 29.33233 24.772 36.41067 7.960667 45.89833 28.28467 5.097667 70.13033 12.85033 29.44033 12.023 22.77967 6.926 8.362 15.28167 13.52433 16.53733 31.838 10.23233 8.268 91.47333 40.92067 12.36 75.059 6.981333 25.25367 31.61067 56.92767 7.083 15.559 21.88967 238.9387 15.914 12.771 21.31667 16.38067 6.314 88.60033 43.318 2.792667 2.752667 17.12667 10.30967 20.27767 40.359 7.979667 23.029 8.47 10.16833 5.342333 10.49233 7.825667 21.02533 65.86733 5.777667 49.53233 12.81233 8.79 11.38633 12.13567 18.746 21.765 28.07033 5.772333 11.90333 9.187667 7.526667 27.34567 21.686 5.664333 2.727 19.21233 5.464 6.437333 5.960667 18.06167 2.539333 3.51 15.31167 46.84667 64.78933 3.596 16.75833 35.59733 37.02633 54.65067 5.197667 12.438 4.820333 21.776 17.25667 20.79733 22.86533 3.046667 24.662 7.951 22.029 32.918 7.603667 14.33467 16.17933 11.03933 6.225667 14.50533 23.46733 8.792667 7.807333 29.746 6.306667 11.28667 8.809 10.73033 3.531333 8.48 0.8883333 22.12067 6.174667 14.356 7.113667 5.639333 74.98367 7.839333 3.158 0 5.134333 0 6.934 3.201 12.918 78.08667 1.752333 5.177333 7.395 7.025 1.506333 19.07367 0 9.925 3.503 3.788 13.76033 7.259 5.081 8.591 23.97033 10.31933 9.197667 0 7.501667 7.014667 2.654667 2.409667 3.867 2.723333 8.232 4.912333 6.318 2.349 1.934333 0.2506667 6.052333 23.34367 3.773667 0.093 2.518667 0.5686667 2.742667 3.633333 7.901333 5.981333 2.414667 2.105667 2.653333 7.077333 2.888 2.993667 6.688 4.237 10.41 7.560667 1.734 9.876 9.321667 2.503 4.064667 5.407667 2.677333 3.311333 0 4.158 19.63133 6.958667 3.617 7.296333 1.742333 0.4486667 0 2.967333 8.351 10.97667 4.931333 2.231667 3.471667 7.922333 3.082 1.651333 2.362667 10.806 5.76 6.261 3.945333 3.743 3.012 2.387667 2.98 1.755667 4.701 1.848333 2.767667 19.41933 1.224333 2.625667 0 1.870667 0.4626667 0 1.403333 1.814333 4.514333 0 5.397667 13.32033 2.961333 2.188333 3.138333 4.864 7.176667 0 3.174667 5.445 1.803333 1.448333 1.584 12.06 2.361 2.965333 2.893667 0.829 1.168333 2.242 3.214 8.255667 7.399 4.021333 1.874 3.013 5.335333 1.322667File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
2883s  1.187667 2.536333 2.772 4.765 0.733 0.5746667 2.15 
2883s 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 
2883s num discordant:  0 
2883s touch test_edgeR
2883s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_DE_analysis.pl  -m Trinity_trans.counts.matrix --method DESeq2 -s samples.txt -o DESeq2_outdir
2883s $VAR1 = {
2883s           'wt_ph8' => [
2883s                         'wt_ph8_1',
2883s                         'wt_ph8_2',
2883s                         'wt_ph8_3'
2883s                       ],
2883s           'wt_GSNO' => [
2883s                          'wt_GSNO_1',
2883s                          'wt_GSNO_2',
2883s                          'wt_GSNO_3'
2883s                        ],
2883s           'wt_37' => [
2883s                        'wt_37_1',
2883s                        'wt_37_2',
2883s                        'wt_37_3'
2883s                      ]
2883s         };
2883s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.Rscript
2883s Got 9 samples, and got: 10 data fields.
2883s 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
2883s Next: TR24|c0_g1_i1	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
2883s 
2883s $VAR1 = {
2883s           'wt_GSNO_3' => 4,
2883s           'wt_GSNO_2' => 6,
2883s           'wt_ph8_3' => 7,
2883s           'wt_ph8_1' => 8,
2883s           'wt_ph8_2' => 9,
2883s           'wt_37_1' => 3,
2883s           'wt_37_3' => 2,
2883s           'wt_GSNO_1' => 5,
2883s           'wt_37_2' => 1
2883s         };
2883s Contrasts to perform are: $VAR1 = [
2883s           [
2883s             'wt_37',
2883s             'wt_GSNO'
2883s           ],
2883s           [
2883s             'wt_37',
2883s             'wt_ph8'
2883s           ],
2883s           [
2883s             'wt_GSNO',
2883s             'wt_ph8'
2883s           ]
2883s         ];
2883s Loading required package: edgeR
2883s Loading required package: limma
2884s Loading required package: DESeq2
2884s Loading required package: S4Vectors
2884s Loading required package: stats4
2884s Loading required package: BiocGenerics
2884s 
2884s Attaching package: ‘BiocGenerics’
2884s 
2884s The following object is masked from ‘package:limma’:
2884s 
2884s     plotMA
2884s 
2884s The following objects are masked from ‘package:stats’:
2884s 
2884s     IQR, mad, sd, var, xtabs
2884s 
2884s The following objects are masked from ‘package:base’:
2884s 
2884s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2884s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2884s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2884s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2884s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
2884s     tapply, union, unique, unsplit, which.max, which.min
2884s 
2885s 
2885s Attaching package: ‘S4Vectors’
2885s 
2885s The following object is masked from ‘package:utils’:
2885s 
2885s     findMatches
2885s 
2885s The following objects are masked from ‘package:base’:
2885s 
2885s     expand.grid, I, unname
2885s 
2885s Loading required package: IRanges
2885s Loading required package: GenomicRanges
2885s Loading required package: GenomeInfoDb
2886s Loading required package: SummarizedExperiment
2886s Loading required package: MatrixGenerics
2886s Loading required package: matrixStats
2886s 
2886s Attaching package: ‘MatrixGenerics’
2886s 
2886s The following objects are masked from ‘package:matrixStats’:
2886s 
2886s     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
2886s     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
2886s     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
2886s     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
2886s     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
2886s     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
2886s     colWeightedMeans, colWeightedMedians, colWeightedSds,
2886s     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
2886s     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
2886s     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
2886s     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
2886s     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
2886s     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
2886s     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
2886s     rowWeightedSds, rowWeightedVars
2886s 
2886s Loading required package: Biobase
2887s Welcome to Bioconductor
2887s 
2887s     Vignettes contain introductory material; view with
2887s     'browseVignettes()'. To cite Bioconductor, see
2887s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2887s 
2887s 
2887s Attaching package: ‘Biobase’
2887s 
2887s The following object is masked from ‘package:MatrixGenerics’:
2887s 
2887s     rowMedians
2887s 
2887s The following objects are masked from ‘package:matrixStats’:
2887s 
2887s     anyMissing, rowMedians
2887s 
2891s converting counts to integer mode
2891s estimating size factors
2891s estimating dispersions
2891s gene-wise dispersion estimates
2892s mean-dispersion relationship
2892s final dispersion estimates
2893s fitting model and testing
2896s null device 
2896s           1 
2896s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.Rscript
2896s Loading required package: edgeR
2896s Loading required package: limma
2896s Loading required package: DESeq2
2896s Loading required package: S4Vectors
2896s Loading required package: stats4
2896s Loading required package: BiocGenerics
2896s 
2896s Attaching package: ‘BiocGenerics’
2896s 
2896s The following object is masked from ‘package:limma’:
2896s 
2896s     plotMA
2896s 
2896s The following objects are masked from ‘package:stats’:
2896s 
2896s     IQR, mad, sd, var, xtabs
2896s 
2896s The following objects are masked from ‘package:base’:
2896s 
2896s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2896s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2896s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2896s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2896s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
2896s     tapply, union, unique, unsplit, which.max, which.min
2896s 
2897s 
2897s Attaching package: ‘S4Vectors’
2897s 
2897s The following object is masked from ‘package:utils’:
2897s 
2897s     findMatches
2897s 
2897s The following objects are masked from ‘package:base’:
2897s 
2897s     expand.grid, I, unname
2897s 
2897s Loading required package: IRanges
2898s Loading required package: GenomicRanges
2898s Loading required package: GenomeInfoDb
2898s Loading required package: SummarizedExperiment
2898s Loading required package: MatrixGenerics
2898s Loading required package: matrixStats
2898s 
2898s Attaching package: ‘MatrixGenerics’
2898s 
2898s The following objects are masked from ‘package:matrixStats’:
2898s 
2898s     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
2898s     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
2898s     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
2898s     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
2898s     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
2898s     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
2898s     colWeightedMeans, colWeightedMedians, colWeightedSds,
2898s     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
2898s     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
2898s     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
2898s     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
2898s     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
2898s     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
2898s     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
2898s     rowWeightedSds, rowWeightedVars
2898s 
2898s Loading required package: Biobase
2899s Welcome to Bioconductor
2899s 
2899s     Vignettes contain introductory material; view with
2899s     'browseVignettes()'. To cite Bioconductor, see
2899s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2899s 
2899s 
2899s Attaching package: ‘Biobase’
2899s 
2899s The following object is masked from ‘package:MatrixGenerics’:
2899s 
2899s     rowMedians
2899s 
2899s The following objects are masked from ‘package:matrixStats’:
2899s 
2899s     anyMissing, rowMedians
2899s 
2903s converting counts to integer mode
2903s estimating size factors
2903s estimating dispersions
2903s gene-wise dispersion estimates
2904s mean-dispersion relationship
2904s final dispersion estimates
2905s fitting model and testing
2907s null device 
2907s           1 
2908s CMD: Rscript Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.Rscript
2908s Loading required package: edgeR
2908s Loading required package: limma
2908s Loading required package: DESeq2
2908s Loading required package: S4Vectors
2908s Loading required package: stats4
2908s Loading required package: BiocGenerics
2908s 
2908s Attaching package: ‘BiocGenerics’
2908s 
2908s The following object is masked from ‘package:limma’:
2908s 
2908s     plotMA
2908s 
2908s The following objects are masked from ‘package:stats’:
2908s 
2908s     IQR, mad, sd, var, xtabs
2908s 
2908s The following objects are masked from ‘package:base’:
2908s 
2908s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2908s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2908s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2908s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2908s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
2908s     tapply, union, unique, unsplit, which.max, which.min
2908s 
2909s 
2909s Attaching package: ‘S4Vectors’
2909s 
2909s The following object is masked from ‘package:utils’:
2909s 
2909s     findMatches
2909s 
2909s The following objects are masked from ‘package:base’:
2909s 
2909s     expand.grid, I, unname
2909s 
2909s Loading required package: IRanges
2910s Loading required package: GenomicRanges
2910s Loading required package: GenomeInfoDb
2910s Loading required package: SummarizedExperiment
2910s Loading required package: MatrixGenerics
2910s Loading required package: matrixStats
2910s 
2910s Attaching package: ‘MatrixGenerics’
2910s 
2910s The following objects are masked from ‘package:matrixStats’:
2910s 
2910s     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
2910s     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
2910s     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
2910s     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
2910s     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
2910s     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
2910s     colWeightedMeans, colWeightedMedians, colWeightedSds,
2910s     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
2910s     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
2910s     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
2910s     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
2910s     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
2910s     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
2910s     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
2910s     rowWeightedSds, rowWeightedVars
2910s 
2910s Loading required package: Biobase
2911s Welcome to Bioconductor
2911s 
2911s     Vignettes contain introductory material; view with
2911s     'browseVignettes()'. To cite Bioconductor, see
2911s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2911s 
2911s 
2911s Attaching package: ‘Biobase’
2911s 
2911s The following object is masked from ‘package:MatrixGenerics’:
2911s 
2911s     rowMedians
2911s 
2911s The following objects are masked from ‘package:matrixStats’:
2911s 
2911s     anyMissing, rowMedians
2911s 
2915s converting counts to integer mode
2915s estimating size factors
2915s estimating dispersions
2916s gene-wise dispersion estimates
2916s mean-dispersion relationship
2916s final dispersion estimates
2917s fitting model and testing
2920s null device 
2920s           1 
2920s cd DESeq2_outdir && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl  \
2920s --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt --order_columns_by_samples_file && \
2920s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt
2920s 
2920s 
2920s ** Found 1783 features as differentially expressed.
2920s 
2920s 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 
2920s CMD: Rscript diffExpr.P0.001_C2.matrix.R
2920s Loading required package: BiocGenerics
2920s 
2920s Attaching package: ‘BiocGenerics’
2920s 
2920s The following objects are masked from ‘package:stats’:
2920s 
2920s     IQR, mad, sd, var, xtabs
2920s 
2920s The following objects are masked from ‘package:base’:
2920s 
2920s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2920s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2920s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2920s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2920s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
2920s     tapply, union, unique, unsplit, which.max, which.min
2920s 
2920s Welcome to Bioconductor
2920s 
2920s     Vignettes contain introductory material; view with
2920s     'browseVignettes()'. To cite Bioconductor, see
2920s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2920s 
2921s 
2921s Attaching package: ‘fastcluster’
2921s 
2921s The following object is masked from ‘package:stats’:
2921s 
2921s     hclust
2921s 
2921s [1] "Reading matrix file."
2922s for plotting:: min.raw: -0.674993513119273 max.raw: 1
2922s Warning messages:
2922s 1: In heatmap.3(sample_cor_for_plot, dendrogram = "both", Rowv = RowV,  :
2922s   Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
2922s 2: In heatmap.3(sample_cor_for_plot, dendrogram = "both", Rowv = RowV,  :
2922s   Discrepancy: Colv is FALSE, while dendrogram is `none'. Omitting column dendogram.
2922s null device 
2922s           1 
2923s for plotting:: min.raw: -7.50284849776958 max.raw: 7.50284849776958
2923s null device 
2923s           1 
2924s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset 
2924s sampleA_mean:  4954.434 1326.5 1046.9 470.179 1833.283 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset) passes test.
2924s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test.
2924s 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 168.4167 15.402 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 
2924s 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 29.664 0.4626667 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 
2924s num discordant:  0 
2924s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset 
2924s 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 37.25567 223.9227 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 66.65833 321.257 497.7577 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 1.851 1001.993 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 21.06767 6.250667 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 21.74467 22.93933 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 
2924s 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 1237.565 498.566 636.1717 1388.008 188.059 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 2983.166 365.304 1573.052 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 59.07767 6554.638 177.7223 111.3283 71.95633 112.4907 205.2823 272.869 62.202 80.658 92.10033 67.32633 136.3853 92.673 92.91767 114.413 578.1793 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 97.74133 143.2053 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 
2924s num discordant:  0 
2924s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset 
2924s 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 File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset) passes test.
2924s 45.54267 20.21567 11.48267 
2924s 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 
2924s num discordant:  0 
2924s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset 
2924s sampleA_mean:  21.39933 88.57 72.55133 7.685 6.167 15.838 15.04567 224.904 40.988 102.2703 31.261 96.61333 103.6867 36.11867 121.0697 509.7623 28.64033 68.104 141.0787 30.97967 55.26267 803.1917 539.652 337.399 98.448 26.51267 76.15267 16.51667 655.8127 37.21967 503.5693 478.7223 46.17067 354.6413 504.111 279.6767 578.8703 10.53633 20.01233 526.2243 409.1913 733.6827 558.1363 4.654333 697.2287 5.762333 7.282667 57.26933 915.841 1275.026 291.1757 35.44767 18.96267 443.633 763.5533 2.713333 16.54033 81.319 620.406 641.1777 903.1557 7.963667 300.087 5.415 4.080333 40.83233 31.92667 125.9483 25.208 88.20633 96.77733 7.252667 4.244 11.583 7.212667 31.97667 850.6397 25.78433 425.357 115.4593 45.412 106.1753 78.96333 11.22367 188.4693 9.434667 223.9227 759.571 24.615 14.71933 31.501 209.5917 48.562 2.398333 47.34533 25.605 89.987 113.9973 691.0767 28.26467 159.4173 11.52 56.797 40.25467 33.62067 670.486 20.97667 171.0287 43.09833 26.208 497.7577 40.27 33.57133 13.98533 22.51133 15.54567 81.34233 2.068 23.04333 22.74167 110.725 50.11167 43.50567 18.76 23.33733 87.317 5.017333 12.993 642.0663 321.257 3.451 47.036 16.528 20.36667 23.127 55.73 37.27233 9.896333 443.3597 51.407 65.027 34.135 86.883 18.754 241.785 12.94133 7.980667 5.627 3.420333 393.3037 37.152 23.94067 260.666 19.92833 6.745333 57.46833 75.469 91.49933 87.42633 5.474667 17.48067 16.899 1.292667 79.21967 29.55 6.546 11.438 4.281667 13.46667 50.469 2.550333 225.8327 15.09333 5.682 39.67767 3.586667 3.078667 52.084 26.715 3.200667 66.65833 2.696667 27.29 26.67967 103.9153 9.969333 16.27833 18.317 9.642 2.280333 25.55733 55.59767 8.043333 6.919333 8.791 74.79833 22.68433 5.016 6.515667 7.059 15.73033 64.82733 15.92433 15.01 3.595333 103.2833 5.733 24.63167 37.25567 21.51767 5.557333 30.828 10.95167 27.48633 62.50533 11.312 18.88733 1.577 5.630333 11.227 7.909333 49.835 16.556 17.19067 1.460333 22.31233 15.18033 2.154 1.919333 2.177333 30.80767 17.96533 24.758 8.807333 14.063 18.233 18.30367 47.42233 2.811 17.221 2.243333 6.819 26.75667 4.745 10.216 10.30533 6.559667 4.766333 29.18933 44.93767 27.59267 44.996 19.11967 2.219333 27.83967 50.97333 4.371 18.62433 2.433333 5.802333 6.812333 7.844 9.735667 28.057 13.08133 23.09367 22.752 11.29367 21.116 3.468 5.931333 12.39433 20.261 26.291 6.455667 22.17067 3.941333 22.93933 12.98 13.65367 13.78833 20.37167 12.753 4.531333 15.08833 4.156333 4.59 7.48 27.94767 16.40367 8.497 7.039 37.255 23.67567 0.713 6.496333 6.980333 20.992 8.162667 8.316667 3.139 11.22367 9.507333 7.107 20.135 4.341667 33.01633 6.527333 18.94267 11.286 3.043 5.615667 12.36433 6.674 20.74967 1.991 31.32 28.45833 6.300667 32.849 42.16967 9.557333 84.312 6.929 2.330333 8.631333 5.895 14.94733 7.412333 0.8066667 44.07433 16.303 22.627 19.73 2.900667 1.911333 27.23133 9.613667 2.534667 77.21567 5.364667 8.077 40.34367 7.163 5.177333 30.424 11.93267 0.4346667 6.524 15.64 19.921 33.50367 28.33667 0.838 11.89067 8.403667 22.996 20.16567 2.592667 9.824333 7.354 4.963667 7.310333 9.767333 1.288 1.688667 8.578333 14.22267 14.78033 13.22967 7.884667 18.30633 11.817 18.33267 25.32233 3.857 8.002 14.06433 39.729 2.723 0.6643333 5.558333 12.40267 12.14267 0.7683333 15.57933 8.393333 17.692 9.773333 10.38333 25.40433 8.173 17.85933 28.43467 27.77367 1.469333 6.380333 35.802 21.06767 13.58 4.676 1.715333 21.69333 8.805333 7.050333 11.758 9.744667 18.23433 17.332 3.424 30.75333 11.994 14.91467 33.10033 7.083333 5.720333 7.216333 6.066 10.12033 9.616 14.16 8.866333 53.09233 7.672667 1.160333 6.248333 7.555333 1.162333 11.59067 2.411 12.76533 5.581333 3.162667 7.394333 6.910667 8.791667 0.1093333 11.36067 5.740333 0.3666667 1.695333 6.863 7.431333 11.21733 3.09 16.06567 5.416333 2.682667 44.679 10.85033 21.88733 6.204 2.976667 5.332667 11.097 0.485 18.93367 6.592 13.23767 4.926 7.585333 1.444 3.541667 20.36133 0.248 5.264 1.363333 8.395 5.603 6.067667 3.762 2.844 1.252 25.089 6.752667 7.766333 9.471667 0.9146667 3.109667 2.605 9.752333 0 0 5.596333 13.50467 10.201 6.861667 8.198 6.983667 1.302333 5.421333 8.351333 161.101 1.448333 2.715 21.32033 6.521 3.294667 2.818 2.745 5.057 1.897333 2.163667 2.14 7.621667 4.058 6.567 13.88733 12.883 7.601333 11.40267 15.09267 0 1.122 2.922 0.01 8.293333 7.325667 4.009 12.67933 1.351667 7.168667 3.765 0 8.038333 3.292 6.625333 23.38367 3.418667 0 1.574667 4.064333 4.638 3.822 18.91833 2.310667 0.4176667 4.053 1.769667 8.223667 36.09 1.281667 3.090333 6.754333 1.851 1.981333 8.255667 7.195333 7.337333 0 4.196 3.425333 0 2.800667 16.116 2.194 6.813333 8.773 5.060667 2.517333 6.512667 4.325333 1.089 0.7146667 2.474333 3.273 1.407667 1.994667 3.696333 4.572333 0.2473333 3.122667 2.883333 6.893667 4.765 3.493 3.293333 1.492667 1.649667 3.179 3.219333 0 1.576667 0 0.7693333 4.387 1.547 1.992333 1.344 4.989667 3.403333 0 1.980333 12.75533 2.347333 0.5473333 3.398 3.570667 2.877333 0.622 0 2.275333 3.733667 11.126 4.611667 0.9123333 7.756333 1.637333 0.409 2.663333 0.676 8.504333 2.337333 0.939 3.988333 2.414667 2.692333 2.448333 2.777667 3.992 1.56 3.319667 4.52 3.021333 2.577667 3.077333 4.451333 4.385333 6.45 2.578333 5.633333 0.4253333 
2924s 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 
2924s num discordant:  0 
2924s validating:  Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset 
2924s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
2924s 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 
2924s 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 27.23467File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test.
2924s  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 
2924s num discordant:  0 
2924s validating:  Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset 
2924s 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 
2924s 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 
2924s num discordant:  0 
2924s File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
2924s touch test_DESeq2
2924s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_DE_analysis.pl  -m Trinity_trans.counts.matrix --method voom -s samples.txt -o voom_outdir
2924s Got 9 samples, and got: 10 data fields.
2924s 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
2924s Next: TR24|c0_g1_i1	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
2924s 
2924s $VAR1 = {
2924s           'wt_ph8_1' => 8,
2924s           'wt_GSNO_2' => 6,
2924s           'wt_ph8_2' => 9,
2924s           'wt_37_2' => 1,
2924s           'wt_GSNO_1' => 5,
2924s           'wt_37_3' => 2,
2924s           'wt_GSNO_3' => 4,
2924s           'wt_37_1' => 3,
2924s           'wt_ph8_3' => 7
2924s         };
2924s $VAR1 = {
2924s           'wt_ph8' => [
2924s                         'wt_ph8_1',
2924s                         'wt_ph8_2',
2924s                         'wt_ph8_3'
2924s                       ],
2924s           'wt_GSNO' => [
2924s                          'wt_GSNO_1',
2924s                          'wt_GSNO_2',
2924s                          'wt_GSNO_3'
2924s                        ],
2924s           'wt_37' => [
2924s                        'wt_37_1',
2924s                        'wt_37_2',
2924s                        'wt_37_3'
2924s                      ]
2924s         };
2924s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.wt_37.vs.wt_GSNO.voom.Rscript
2924s Contrasts to perform are: $VAR1 = [
2924s           [
2924s             'wt_37',
2924s             'wt_GSNO'
2924s           ],
2924s           [
2924s             'wt_37',
2924s             'wt_ph8'
2924s           ],
2924s           [
2924s             'wt_GSNO',
2924s             'wt_ph8'
2924s           ]
2924s         ];
2924s Loading required package: limma
2926s null device 
2926s           1 
2926s CMD: Rscript Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.wt_37.vs.wt_ph8.voom.Rscript
2926s Loading required package: limma
2928s null device 
2928s           1 
2928s CMD: Rscript Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.wt_GSNO.vs.wt_ph8.voom.Rscript
2928s Loading required package: limma
2929s null device 
2929s           1 
2929s cd voom_outdir && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl  \
2929s --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt && \
2929s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt
2930s 
2930s 
2930s ** Found 1817 features as differentially expressed.
2930s 
2930s 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
2930s CMD: Rscript diffExpr.P0.001_C2.matrix.R
2930s Loading required package: BiocGenerics
2930s 
2930s Attaching package: ‘BiocGenerics’
2930s 
2930s The following objects are masked from ‘package:stats’:
2930s 
2930s     IQR, mad, sd, var, xtabs
2930s 
2930s The following objects are masked from ‘package:base’:
2930s 
2930s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2930s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2930s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2930s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2930s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
2930s     tapply, union, unique, unsplit, which.max, which.min
2930s 
2930s Welcome to Bioconductor
2930s 
2930s     Vignettes contain introductory material; view with
2930s     'browseVignettes()'. To cite Bioconductor, see
2930s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2930s 
2931s [1] "Reading matrix file."
2931s 
2931s Attaching package: ‘fastcluster’
2931s 
2931s The following object is masked from ‘package:stats’:
2931s 
2931s     hclust
2931s 
2931s for plotting:: min.raw: -0.680559894057534 max.raw: 1
2931s null device 
2931s           1 
2932s for plotting:: min.raw: -7.50284849776958 max.raw: 7.50284849776958
2932s null device 
2932s           1 
2933s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_37-UP.subset 
2933s 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 
2933s 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 
2933s num discordant:  0 
2933s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset 
2933s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_37-UP.subset) passes test.
2933s 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 
2934s sampleB_mean:  6464.644 7520.41 7779.492 6944.853 1492.051 2827.345 1331.648 9939.373 7181.47 1438.471 10849.9 2550.414 971.4367 11165.49 5346.478 1076.978 2449.757 3982.392 6705.697 1007.03 5874.642 347.4017 6156.043 6887.084 440.9727 5515.698 8614.152 8614.152 4540.328 5036.385 4809.412 973.0083 1506.715 7405.14 5974.238 3104.744 8313.711 8625.824 3325.992 5589.41 819.1427 3398.294 7596.105 303.273 876.8277 2510.784 501.0717 217.5877 512.042 12136.75 147.2877 2649.173 850.5097 155.6753 318.3057 493.2167 193.995 8726.054 1237.565 11956.17 803.7297 1192.947 4624.974 395.6523 4978.607 10695.83 341.9023 3101.543 381.4813 176.1237 324.8553 5311.835 1781.496 12803.12 9160.812 286.7303 10005.84 2806.072 644.756 721.2523 297.5633 337.5617 722.7793 7921.826 188.059 510.9113 3043.903 880.4753 592.331 11807.78 8077.68 5150.462 1147.187 178.331 1388.008 369.4417 568.9407 7137.863 4181.758 14596.83 9231.562 820.1 227.1767 1183.775 624.4283 3135.76 165.5147 98.27667 374.99 126.265 464.656 437.7077 498.566 7646.521 340.8923 2069.238 501.203 223.6213 347.1993 2813.865 330.2803 497.3057 3606.195 3477.406 210.5073 237.9167 229.8227 636.1717 265.4807 303.588 234.8707 464.25 59.968 88.77667 1727.754 277.6277 568.3683 2899.79 1232.959 7998.991 221.5063 135.6287 4052.112 784.5 437.8937 242.2357 198.0453 177.0987 151.089 204.598 209.5997 136.0917 309.0137 318.668 366.6233 53.11833 365.304 205.964 5402.498 7391.381 248.7967 5955.872 3497.592 304.1167 96.888 102.4913 224.959 365.9053 383.3883 183.432 954.507 146.225 244.213 228.616 346.0203 159.9217 617.5097 322.6313 124.821 566.3103 130.7987 744.834 473.468 41.92667 221.3943 376.801 257.8713 171.415 169.5693 58.786 363.4697 12057.81 4659.391 1314.765 76.629 93.961 79.78767 361.7567 208.997 1374.415 87.30767 227.959 201.1477 153.6373 297.5293 204.0893 171.2443 88.84733 1538.062 2636.168 84.19433 794.7277 261.1813 434.0653 219.043 146.7367 306.1523 324.095 254.0923 728.6047 1485.8 204.688 10466.26 92.66933 139.8577 133.1137 243.0527 199.25 134.7863 396.4167 259.974 31019.62 102.9103 55.56067 91.93733 190.3363 196.2657 210.276 120.016 307.597 2478.864 434.0367 160.6447 65.82467 1924.887 92.04867 148.3807 125.9207 110.12 217.828 186.3673 112.8707 92.801 102.8277 85.369 332.1927 109.1297 317.4007 106.9733 118.4783 162.353 132.86 279.8187 88.724 115.6383 145.871 94.855 2983.166 53.67933 163.2497 107.6607 288.2643 63.51467 44.52667 104.7473 1573.052 91.36867 130.4647 129.359 189.81 49.84633 38.50333 132.997 155.6507 198.031 56.084 189.876 241.8647 92.14267 138.9953 221.9553 141.1233 383.105 3680.324 240.9067 166.719 108.0163 502.0593 219.1713 79.23 51.48067 72.27033 147.5143 327.728 434.5497 251.6407 293.4293 506.512 150.83 165.6487 1190.783 199.5333 72.04033 71.07333 188.654 54.17467 217.945 109.0163 446.5917 101.2043 89.19033 264.5573 6554.638 404.8233 177.6103 244.312 451.6893 65.022 391.7213 94.036 381.073 160.461 125.6427 175.727 102.4957 142.4997 114.7247 91.96267 313.5353 80.658 160.033 139.4217 55.31033 138.7943 66.28233 65.14433 97.74133 67.32633 88.20067 48.662 71.95633 75.13167 98.59367 111.3283 42.94067 79.15267 112.4907 143.6177 138.8203 82.77467 83.32767 57.92467 92.10033 147.9097 55.42833 92.673 615.4837 329.0943 177.7223 86.82867 117.3687 272.869 176.1103 72.229 123.7103 205.2823 65.265 23095.85 63.39167 98.42267 143.2053 52.40167 36.84367 30.305 189.338 68.93667 70.82967 136.3853 1768.526 97.67333 59.07767 126.6667 54.697 78.15767 63.519 54.28 629.935 114.413 98.25867 51.40267 33.64933 61.75633 62.202 47.69867 106.367 64.48933 61.927 58.84033 31.92033 44.59133 59.70833 12433.72 108.9977 66.58633 101.2333 37.13833 92.91767 92.354 67.97633 69.31567 185.3687 75.314 59.309 205.7273 44.65167 578.1793 1437.071 565.0517 49.55567 57.289 71.83833 56.87433 80.30267 89.473 25.16133 84.09433 64.96333 39.14833 97.91867 26.105 359.4497 59.017 91.34767 20.836 37.861 40.01867 269.8203 43.553 36.83567 51.20733 63.275 74.47967 28.11233 72.092 57.89033 31.81733 29.19933 180.145 17.67167 27.42533 92.58367 53.35367 45.43467 42.02167 86.666 29.412 38.239 71.77333 50.94033 70.23367 70.48667 24.105 36.129 51.208 654.0063 104.9537 16.98933 21.31667 60.39433 38.35733 36.76167 100.9357 24.998 60.909 31.64467 49.809 60.34067 558.288 105.9517 44.80233 58.52433 40.58467 374.3023 40.88467 65.641 37.373 43.199 23.09333 49.184 58.53467 83.02567 42.55233 67.40867 58.72433 49.53233 44.57067 46.01667 74.76 37.18267 94.084 39.439 32.39167 41.25767 77.42067 28.99667 23.031 323.135 82.208 95.03067 52.62167 48.09067 63.80367 61.049 52.59533 118.5717 17.978 22.795 343.3797 275.1827 284.8557 25.818 38.56967 170.258 33.71767 45.68133 22.759 134.3513 170.7703 147.841 56.735 19.01033 64.17467 89.41967 28.08767 19.87967 50.66867 50.351 59.187 63.14133 63.43233 35.30367 40.58733 17.20333 21.37133 21.26833 72.57967 40.14133 24.42933 27.15533 28.618 33.96667 80.83067 18.746 19.069 101.7453 57.38933 12.81233 26.59233 25.20967 16.69733 39.557 134.6853 46.573 16.53733 31.40267 81.03933 17.666 18.67167 16.98933 31.359 50.767 34.963 38.06967 82.00433 43.21967 541.9867 79.93733 17.60767 21.58933 13.31667 9.165333 45.292 15.914 200.7123 13.12667 16.692 16.39933 62.14133 38.21633 130.2143 18.98967 21.925 17.79667 12.13567 79.05433 125.1613 23.01233 29.38867 58.21167 42.533 51.753 23.8 10.878 70.339 37.33167 122.654 8.173667 24.04433 37.97 14.291 55.27767 11.24133 37.89133 23.558 67.874 10.06533 43.66433 139.358 33.81667 37.642 24.348 11.09467 69.305 8.385 47.25833 28.28967 17.76433 20.035 63.401 48.78233 12.62967 35.64 22.82667 9.080667 11.03933 92.552 1.073 15.776 13.166 45.16467 23.05967 37.25433 24.88967 22.41933 27.504 45.16833 22.33433 22.85333 12.07167 76.51933 19.075 34.98133 14.71567 21.97667 23.06333 11.718 133.2117 26.364 18.868 19.56367 17.268 11.69767 23.021 
2934s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_GSNO.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test.
2934s num discordant:  0 
2934s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_37-UP.subset 
2934s sampleA_mean:  6030.232 1681.385 1407.266 5797.692 1833.283 20787.35 1046.9 2191.464 1326.5 4954.434 5495.505 4913.275 12222.46 4191.816 2602.336 2635.243 944.0123 1512.754 1013.064 1371.045 982.539 559.8297 335.7477 637.4673 1272.664 1265.232 1751.765 1445.705 521.84 887.2083 1532.142 326.0873 1233.492 2002.536 1939.628 3549.085 1593.001 4784.861 562.1487 470.179 1262.588 810.3883 1718.763 5645.434 499.8527 1037.645 388.648 405.4877 1707.219 581.2863 3468.578 647.4437 925.3123 178.6107 258.5643 933.0403 1031.742 371.296 1348.496 393.785 116.9527 15024.4 999.5363 335.637 335.2157 1088.069 564.1773 1753.538 405.9907 533.844 460.3903 1091.041 425.4187 104.2153 4713.887 1933.215 154.4447 1640.267 387.8127 620.238 923.62 296.1627 36600.33 1816.62 2446.14 825.5967 838.8547 1291.39 194.6923 1656.826 298.6353 1179.723 521.2813 344.3147 604.7417 2017.126 159.0503 2237.79 531.0443 876.645 581.914 772.306 610.589 494.789 508.1423 872.2057 1707.261 664.8137 252.8977 337.767 1547.728 337.406 150.8137 133.8673 1030.087 568.889 482.3557 1434.927 1120.621 244.4597 234.695 233.2683 363.4713 5637.134 176.112 480.5827 1756.628 147.324 168.438 349.218 356.3497 378.0157 594.819 762.2617 2891.881 244.753 272.6143 85.82433 350.3023 1125.723 146.7767 210.486 201.4867 198.9307 114.485 156.591 182.1447 435.0017 991.437 432.0453 563.9263 176.9843 241.211 322.1607 368.628 219.039 1412.697 114.123 5395.606 209.749 407.6713 122.4237 1198.79 502.9777 71.71033 323.746 617.5563 310.3323 116.1613 99.45067 300.2583 240.267 719.3537 125.2723 854.0897 590.469 164.083 109.0817 1315.006 100.0037 89.249 89.41233 177.4467 189.715 97.82467 207.939 437.1223 122.591 770.6237 198.061 207.397 183.172 316.5037 128.0267 324.5383 91.99833 354.7773 389.129 164.5937 127.1483 60.22767 328.3217 161.1783 567.2883 63.90033 665.289 407.805 105.1747 132.971 734.0483 62.56033 1229.376 335.4993 300.3533 294.269 168.189 199.325 104.0613 78.31633 206.046 84.98533 132.1053 499.693 160.8853 210.2437 129.574 122.177 87.49733 250.2393 98.94267 236.6537 471.4763 115.35 519.577 173.3993 172.982 124.4867 181.09 2465.916 59.607 280.7067 60.025 81.80933 154.7137 562.891 291.7607 421.348 169.0567 721.5107 93.672 62.65367 310.3963 94.07567 76.27033 66.11467 55.68233 94.133 98.85333 363.302 278.785 603.3643 113.344 90.65667 105.6967 171.9977 136.4807 156.8307 40.38733 204.4367 3561.451 212.7377 214.102 93.57967 46.29267 62.81 103.573 80.98433 78.67633 305.3177 304.6523 66.544 2036.308 77.01533 53.23867 66.88467 52.74467 1557.898 120.7347 1505.046 95.84833 135.433 51.06833 471.7457 38.966 781.6647 38.21567 54.279 86.272 64.515 35.384 32.07433 32.60533 194.3693 187.0867 971.5327 50.39 56.34967 47.40267 97.46133 3088.486 1606.153 33.614 26.77667 56.42633 47.17133 71.85 27.49133 69.30367 233.2737 158.4977 144.1087 407.7717 74.26433 44.67767 73.156 31.01767 131.435 87.15633 40.76933 44.27933 630.4887 71.55767 86.26767 30.31033 50.27133 49.19267 40.022 93.98167 16.066 42.259 51.916 6075.931 751.6327 69.90667 37.93767 101.362 34.524 35.92467 354.898 82.45067 37.746 425.4893 171.2653 280.1693 42.52667 56.986 58.77867 56.78633 47.12267 51.36633 114.1953 38.41333 26.93367 84.101 58.726 163.5027 42.42 27.86967 26.74467 52.054 70.90433 48.80533 41.489 141.5087 19.36133 34.55067 142.1963 32.87767 19.379 43.001 51.68567 42.69267 69.761 52.49167 45.27567 115.2073 7.951667 27.10933 51.49667 84.52867 4534.064 269.428 38.71367 209.263 24.04867 59.42133 36.44033 31.80833 20.94233 28.112 28.092 26.72567 31.895 32.359 36.69767 20.61433 45.48233 43.59833 38.467 132.0313 66.32833 59.42267 33.66067 20.87967 22.01133 13.58767 13.46233 14.442 19.87867 45.49933 24.69267 23.94367 496.4993 27.92067 56.72833 23.62733 73.985 12.36533 40.90567 13.02633 28.60833 14.06933 37.072 23.51567 32.296 27.81033 10.913 30.83533 18.52533 26.52667 29.40667 36.76933 28.27267 87.54867 27.07933 20.89067 41.65 13.554 18.73767 26.41767 15.976 44.083 16.59667 20.15333 23.038 45.54267 18.127 25.49633 27.188 22.07333 36.86033 12.43333 27.52167 68.59733 20.84167 
2934s 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 
2934s num discordant:  0 
2934s validating:  Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset 
2934s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_37-UP.subset) passes test.
2934s 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 
2934s File: (Trinity_trans.counts.matrix.wt_37_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
2934s 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 
2934s num discordant:  0 
2934s validating:  Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset 
2934s sampleA_mean:  4624.974 1506.715 1636.976 440.9727 1101.219 876.8277 12470.43 2550.414 1781.496 512.042 324.8553 871.6373 707.8263 493.2167 834.608 177.0987 217.5877 347.4017 768.306 645.4617 339.8283 850.5097 3211.031 621.286 198.0453 514.415 411.447 501.203 1098.868 3078.184 222.09 189.5647 95.89333 510.9113 620.017 646.6133 429.5973 224.469 306.1523 1192.947 474.0487 1003.238 1494.298 900.1817 856.7063 374.99 244.213 623.5437 173.88 689.711 237.177 211.7417 646.864 204.598 378.627 132.9247 257.3087 198.031 2373.043 97.24867 166.336 138.8203 109.0163 153.4527 116.0807 661.7387 194.0203 189.876 151.8027 188.654 149.5763 75.79967 328.0923 276.1017 506.512 272.869 161.0497 202.739 37.50533 92.354 215.8967 194.2893 2633.716 103.0963 278.7853 54.95833 112.168 175.2467 53.598 63.519 59.07767 103.6453 100.247 214.853 55.41567 91.645 114.2777 131.159 374.3023 72.98133 499.6263 46.03533 88.61667 45.62033 55.17567 615.4837 106.367 63.24267 80.30267 583.86 82.208 51.208 322.6313 160.284 58.90833 565.0517 112.6127 103.33 541.9867 43.62667 30.70067 39.745 75.16967 36.49633 46.59433 94.455 99.289 227.2843 170.258 189.338 137.7607 40.44433 39.40267 39.44033 578.1793 52.59533 63.80367 28.455 83.27833 32.245 25.087 69.91033 28.618 41.25767 13.208 82.00433 40.18733 29.69867 27.874 37.18267 42.52533 50.351 43.80133 19.68333 35.30367 72.777 50.66867 72.57967 81.69967 124.9103 25.539 50.767 36.466 24.83067 134.6853 7.618667 75.28167 147.841 25.74867 45.16833 31.79067 31.40267 48.78233 23.51433 33.46233 79.93733 63.05533 31.89567 63.71067 18.93167 36.90167 23.01233 28.191 29.06367 59.28433 38.06967 76.51933 18.83133 22.33433 58.47233 19.622 18.868 19.09633 68.14433 69.305 101.7453 48.16367 26.44133 22.32333 29.71933 92.552 57.61033 27.69933 23.021 56.21533 28.387 43.573 45.292 26.81733 20.62167 122.654 52.69467 48.025 72.11233 24.891 67.73133 22.708 27.838 55.27767 49.08533 24.47467 22.96933 37.281 11.958 36.46133 57.80667 58.21167 19.95933 48.198 31.779 23.05967 22.16333 23.8 23.558 28.69233 45.90233 
2934s 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 File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_GSNO-UP.subset) passes test.
2934s 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 
2934s num discordant:  0 
2934s validating:  Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset 
2934s 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 
2934s sampleB_mean:  2830.628 1202.982 4216.251 2415.454 339.544 809.747 968.2863 5398.857 3709.705 2786.993 3756.434 461.5343 317.4807 4004.8 2355.907 13329.63 3506.467 2001.57 2047.901 266.1853 807.5603 1242.884 686.1263 878.6043 953.5553 513.784 501.3557 317.8843 222.0223 574.6353 926.6357 203.078 805.275 843.2847 1524.761 303.08 641.6557 208.1393 562.3953 256.6427 279.329 786.1327 468.317 401.8723 224.5063 731.863 371.2327 1012.972 573.2667 255.0223 265.6093 310.312 255.8583 290.862 255.2837 378.7327 157.5777 205.6727 116.6347 720.0863 166.8767 145.604 4759.337 1440.661 1576.856 148.789 178.71 166.0277 132.4173 1082.98 125.2547 387.0143 584.575 137.7833 121.5623 195.216 1109.48 320.243 286.777 158.383 263.0527 59.23867 168.2893 156.2033 151.719 120.8867 160.5167 232.1147 124.6713 585.796 58.96367 496.8353 1834.421 148.7563 161.1673 91.18133 109.3147 150.3003 477.213 148.6807 163.1987 156.0383 143.3147 178.2697 151.599 92.061 278.7393 311.44 41.78967 163.021 31.73 194.1133 177.154 213.8997 119.8297 51.73767 90.957 57.44367 219.6953 161.4237 194.3873 301.9357 332.2983 253.0167 109.0193 83.61967 174.6973 145.137 405.776 98.33933 110.8993 69.18967 117.851 160.1683 91.509 41.93 437.7257 143.0897 70.221 85.78933 53.655 143.872 188.56 195.2947 101.4477 118.1207 108.837 46.842 113.004 285.3807 193.3587 67.408 48.96533 87.65567 126.6913 64.15933 127.5543 138.9263 36.76567 109.6677 82.68433 141.442 91.739 263.5397 102.0507 54.097 96.804 24.80467 99.863 136.4563 64.25433 51.723 60.90233 179.874 216.4093 90.427 141.0183 230.7707 682.0817 71.949 76.82 91.49033 63.62167 71.81167 170.7463 93.09033 27.192 27.296 50.22033 29.00467 29.627 97.60633 96.94267 107.2877 130.4127 44.69833 47.31267 127.9993 94.78533 39.086 84.001 191.0543 55.476 56.05633 96.91167 112.8043 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 
2934s num discordant:  0 
2934s File: (Trinity_trans.counts.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.P0.001_C2.wt_ph8-UP.subset) passes test.
2934s touch test_voom
2934s /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/PtR -m Trinity_trans.TMM.EXPR.matrix -s samples.txt --heatmap --sample_cor_matrix --log2 --save
2934s CMD: Rscript Trinity_trans.TMM.EXPR.matrix.R
2934s Loading required package: BiocGenerics
2934s 
2934s Attaching package: ‘BiocGenerics’
2934s 
2934s The following objects are masked from ‘package:stats’:
2934s 
2934s     IQR, mad, sd, var, xtabs
2934s 
2934s The following objects are masked from ‘package:base’:
2934s 
2934s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2934s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2934s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2934s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2934s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
2934s     tapply, union, unique, unsplit, which.max, which.min
2934s 
2934s Welcome to Bioconductor
2934s 
2934s     Vignettes contain introductory material; view with
2934s     'browseVignettes()'. To cite Bioconductor, see
2934s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2934s 
2935s 
2935s Attaching package: ‘fastcluster’
2935s 
2935s The following object is masked from ‘package:stats’:
2935s 
2935s     hclust
2935s 
2935s [1] "Reading matrix file."
2936s for plotting:: min.raw: 0.647032826340685 max.raw: 1
2936s null device 
2936s           1 
2941s for plotting:: min.raw: 0 max.raw: 15.3986319455363
2941s null device 
2941s           1 
2951s touch test_PtR_heatmap
2951s ./validate_results.pl
2951s make[2]: Leaving directory '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example'
2951s DESeq2_outdir/diffExpr.P0.001_C2.matrix, count: 1784 DE features OK.
2951s edgeR_outdir/diffExpr.P0.001_C2.matrix, count: 2063 DE features OK.
2951s voom_outdir/diffExpr.P0.001_C2.matrix, count: 1818 DE features OK.
2951s Running example in Spombe_example...
2951s make[2]: Entering directory '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example'
2951s /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
2951s Got 4 samples, and got: 5 data fields.
2951s $VAR1 = {
2951s           'heatshock' => [
2951s                            'hs_rep1'
2951s                          ],
2951s           'log_growth' => [
2951s                             'log_rep1'
2951s                           ],
2951s           'diauxic_shift' => [
2951s                                'ds_rep1'
2951s                              ],
2951s           'plateau' => [
2951s                          'plat_rep1'
2951s                        ]
2951s         };
2951s CMD: Rscript Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.diauxic_shift.vs.heatshock.EdgeR.Rscript
2951s Header: ds_rep1	hs_rep1	log_rep1	plat_rep1
2951s Next: TRINITY_DN5555_c0_g1	0.00	0.00	0.00	0.00
2951s 
2951s $VAR1 = {
2951s           'hs_rep1' => 2,
2951s           'plat_rep1' => 4,
2951s           'ds_rep1' => 1,
2951s           'log_rep1' => 3
2951s         };
2951s Contrasts to perform are: $VAR1 = [
2951s           [
2951s             'diauxic_shift',
2951s             'heatshock'
2951s           ],
2951s           [
2951s             'diauxic_shift',
2951s             'log_growth'
2951s           ],
2951s           [
2951s             'diauxic_shift',
2951s             'plateau'
2951s           ],
2951s           [
2951s             'heatshock',
2951s             'log_growth'
2951s           ],
2951s           [
2951s             'heatshock',
2951s             'plateau'
2951s           ],
2951s           [
2951s             'log_growth',
2951s             'plateau'
2951s           ]
2951s         ];
2951s Loading required package: edgeR
2951s Loading required package: limma
2951s null device 
2951s           1 
2951s CMD: Rscript Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.diauxic_shift.vs.log_growth.EdgeR.Rscript
2951s Loading required package: edgeR
2951s Loading required package: limma
2952s null device 
2952s           1 
2952s CMD: Rscript Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.diauxic_shift.vs.plateau.EdgeR.Rscript
2952s Loading required package: edgeR
2952s Loading required package: limma
2953s null device 
2953s           1 
2953s CMD: Rscript Trinity_genes.counts.matrix.heatshock_vs_log_growth.heatshock.vs.log_growth.EdgeR.Rscript
2953s Loading required package: edgeR
2953s Loading required package: limma
2953s null device 
2953s           1 
2953s CMD: Rscript Trinity_genes.counts.matrix.heatshock_vs_plateau.heatshock.vs.plateau.EdgeR.Rscript
2953s Loading required package: edgeR
2953s Loading required package: limma
2954s null device 
2954s           1 
2954s CMD: Rscript Trinity_genes.counts.matrix.log_growth_vs_plateau.log_growth.vs.plateau.EdgeR.Rscript
2954s Loading required package: edgeR
2954s Loading required package: limma
2955s null device 
2955s           1 
2955s cd edgeR_genes && /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl -m ../Trinity_genes.TMM.EXPR.matrix \
2955s         -s ../samples.txt  --examine_GO_enrichment --GO_annots ../Trinotate_report.xls.gene_ontology --gene_lengths ../Trinity_genes.lengths && \
2955s            /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/validate_UP_subset.Rscript ../samples.txt
2955s 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 
2955s Loading required package: BiasedUrn
2955s Loading required package: geneLenDataBase
2965s 
2965s Loading required package: AnnotationDbi
2965s Loading required package: stats4
2965s Loading required package: BiocGenerics
2965s 
2965s Attaching package: ‘BiocGenerics’
2965s 
2965s The following objects are masked from ‘package:stats’:
2965s 
2965s     IQR, mad, sd, var, xtabs
2965s 
2965s The following objects are masked from ‘package:base’:
2965s 
2965s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2965s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2965s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2965s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2965s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
2965s     tapply, union, unique, unsplit, which.max, which.min
2965s 
2965s Loading required package: Biobase
2965s Welcome to Bioconductor
2965s 
2965s     Vignettes contain introductory material; view with
2965s     'browseVignettes()'. To cite Bioconductor, see
2965s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2965s 
2965s Loading required package: IRanges
2965s Loading required package: S4Vectors
2965s 
2965s Attaching package: ‘S4Vectors’
2965s 
2965s The following object is masked from ‘package:geneLenDataBase’:
2965s 
2965s     unfactor
2965s 
2965s The following object is masked from ‘package:utils’:
2965s 
2965s     findMatches
2965s 
2965s The following objects are masked from ‘package:base’:
2965s 
2965s     expand.grid, I, unname
2965s 
2967s Processing category: custom_list
2967s Using manually entered categories.
2967s Calculating the p-values...
2968s 'select()' returned 1:1 mapping between keys and columns
2968s 
2968s 
2968s Done.
2968s 
2968s 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 
2968s Loading required package: BiasedUrn
2968s Loading required package: geneLenDataBase
2978s 
2978s Loading required package: AnnotationDbi
2978s Loading required package: stats4
2978s Loading required package: BiocGenerics
2978s 
2978s Attaching package: ‘BiocGenerics’
2978s 
2978s The following objects are masked from ‘package:stats’:
2978s 
2978s     IQR, mad, sd, var, xtabs
2978s 
2978s The following objects are masked from ‘package:base’:
2978s 
2978s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2978s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2978s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2978s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2978s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
2978s     tapply, union, unique, unsplit, which.max, which.min
2978s 
2978s Loading required package: Biobase
2978s Welcome to Bioconductor
2978s 
2978s     Vignettes contain introductory material; view with
2978s     'browseVignettes()'. To cite Bioconductor, see
2978s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2978s 
2978s Loading required package: IRanges
2978s Loading required package: S4Vectors
2978s 
2978s Attaching package: ‘S4Vectors’
2978s 
2978s The following object is masked from ‘package:geneLenDataBase’:
2978s 
2978s     unfactor
2978s 
2978s The following object is masked from ‘package:utils’:
2978s 
2978s     findMatches
2978s 
2978s The following objects are masked from ‘package:base’:
2978s 
2978s     expand.grid, I, unname
2978s 
2980s Processing category: custom_list
2980s Using manually entered categories.
2980s Calculating the p-values...
2980s 'select()' returned 1:1 mapping between keys and columns
2981s 
2981s 
2981s Done.
2981s 
2981s 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 
2981s Loading required package: BiasedUrn
2981s Loading required package: geneLenDataBase
2991s 
2991s Loading required package: AnnotationDbi
2991s Loading required package: stats4
2991s Loading required package: BiocGenerics
2991s 
2991s Attaching package: ‘BiocGenerics’
2991s 
2991s The following objects are masked from ‘package:stats’:
2991s 
2991s     IQR, mad, sd, var, xtabs
2991s 
2991s The following objects are masked from ‘package:base’:
2991s 
2991s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
2991s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
2991s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
2991s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
2991s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
2991s     tapply, union, unique, unsplit, which.max, which.min
2991s 
2991s Loading required package: Biobase
2991s Welcome to Bioconductor
2991s 
2991s     Vignettes contain introductory material; view with
2991s     'browseVignettes()'. To cite Bioconductor, see
2991s     'citation("Biobase")', and for packages 'citation("pkgname")'.
2991s 
2991s Loading required package: IRanges
2991s Loading required package: S4Vectors
2991s 
2991s Attaching package: ‘S4Vectors’
2991s 
2991s The following object is masked from ‘package:geneLenDataBase’:
2991s 
2991s     unfactor
2991s 
2991s The following object is masked from ‘package:utils’:
2991s 
2991s     findMatches
2991s 
2991s The following objects are masked from ‘package:base’:
2991s 
2991s     expand.grid, I, unname
2991s 
2993s Processing category: custom_list
2993s Using manually entered categories.
2993s Calculating the p-values...
2993s 'select()' returned 1:1 mapping between keys and columns
2993s 
2993s 
2993s Done.
2993s 
2993s 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 
2993s Loading required package: BiasedUrn
2993s Loading required package: geneLenDataBase
3003s 
3003s Loading required package: AnnotationDbi
3003s Loading required package: stats4
3003s Loading required package: BiocGenerics
3003s 
3003s Attaching package: ‘BiocGenerics’
3003s 
3003s The following objects are masked from ‘package:stats’:
3003s 
3003s     IQR, mad, sd, var, xtabs
3003s 
3003s The following objects are masked from ‘package:base’:
3003s 
3003s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3003s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3003s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3003s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3003s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3003s     tapply, union, unique, unsplit, which.max, which.min
3003s 
3003s Loading required package: Biobase
3003s Welcome to Bioconductor
3003s 
3003s     Vignettes contain introductory material; view with
3003s     'browseVignettes()'. To cite Bioconductor, see
3003s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3003s 
3003s Loading required package: IRanges
3003s Loading required package: S4Vectors
3004s 
3004s Attaching package: ‘S4Vectors’
3004s 
3004s The following object is masked from ‘package:geneLenDataBase’:
3004s 
3004s     unfactor
3004s 
3004s The following object is masked from ‘package:utils’:
3004s 
3004s     findMatches
3004s 
3004s The following objects are masked from ‘package:base’:
3004s 
3004s     expand.grid, I, unname
3004s 
3005s Processing category: custom_list
3005s Using manually entered categories.
3005s Calculating the p-values...
3006s 'select()' returned 1:1 mapping between keys and columns
3006s 
3006s 
3006s Done.
3006s 
3006s CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../Trinotate_report.xls.gene_ontology  --lengths ../Trinity_genes.lengths --genes_single_factor Trinity_genes.counts.matrix.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 
3006s Loading required package: BiasedUrn
3006s Loading required package: geneLenDataBase
3016s 
3016s Loading required package: AnnotationDbi
3016s Loading required package: stats4
3016s Loading required package: BiocGenerics
3016s 
3016s Attaching package: ‘BiocGenerics’
3016s 
3016s The following objects are masked from ‘package:stats’:
3016s 
3016s     IQR, mad, sd, var, xtabs
3016s 
3016s The following objects are masked from ‘package:base’:
3016s 
3016s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3016s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3016s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3016s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3016s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3016s     tapply, union, unique, unsplit, which.max, which.min
3016s 
3016s Loading required package: Biobase
3016s Welcome to Bioconductor
3016s 
3016s     Vignettes contain introductory material; view with
3016s     'browseVignettes()'. To cite Bioconductor, see
3016s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3016s 
3016s Loading required package: IRanges
3016s Loading required package: S4Vectors
3016s 
3016s Attaching package: ‘S4Vectors’
3016s 
3016s The following object is masked from ‘package:geneLenDataBase’:
3016s 
3016s     unfactor
3016s 
3016s The following object is masked from ‘package:utils’:
3016s 
3016s     findMatches
3016s 
3016s The following objects are masked from ‘package:base’:
3016s 
3016s     expand.grid, I, unname
3016s 
3020s Warning message:
3020s In pcls(G) : initial point very close to some inequality constraints
3020s Processing category: custom_list
3020s Using manually entered categories.
3020s Calculating the p-values...
3021s 'select()' returned 1:1 mapping between keys and columns
3022s 
3022s 
3022s Done.
3022s 
3022s 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 
3022s Loading required package: BiasedUrn
3022s Loading required package: geneLenDataBase
3032s 
3032s Loading required package: AnnotationDbi
3032s Loading required package: stats4
3032s Loading required package: BiocGenerics
3032s 
3032s Attaching package: ‘BiocGenerics’
3032s 
3032s The following objects are masked from ‘package:stats’:
3032s 
3032s     IQR, mad, sd, var, xtabs
3032s 
3032s The following objects are masked from ‘package:base’:
3032s 
3032s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3032s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3032s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3032s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3032s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3032s     tapply, union, unique, unsplit, which.max, which.min
3032s 
3032s Loading required package: Biobase
3032s Welcome to Bioconductor
3032s 
3032s     Vignettes contain introductory material; view with
3032s     'browseVignettes()'. To cite Bioconductor, see
3032s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3032s 
3032s Loading required package: IRanges
3032s Loading required package: S4Vectors
3032s 
3032s Attaching package: ‘S4Vectors’
3032s 
3032s The following object is masked from ‘package:geneLenDataBase’:
3032s 
3032s     unfactor
3032s 
3032s The following object is masked from ‘package:utils’:
3032s 
3032s     findMatches
3032s 
3032s The following objects are masked from ‘package:base’:
3032s 
3032s     expand.grid, I, unname
3032s 
3037s Processing category: custom_list
3037s Using manually entered categories.
3037s Calculating the p-values...
3038s 'select()' returned 1:1 mapping between keys and columns
3038s 
3038s 
3038s Done.
3038s 
3038s 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 
3038s Loading required package: BiasedUrn
3038s Loading required package: geneLenDataBase
3049s 
3049s Loading required package: AnnotationDbi
3049s Loading required package: stats4
3049s Loading required package: BiocGenerics
3049s 
3049s Attaching package: ‘BiocGenerics’
3049s 
3049s The following objects are masked from ‘package:stats’:
3049s 
3049s     IQR, mad, sd, var, xtabs
3049s 
3049s The following objects are masked from ‘package:base’:
3049s 
3049s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3049s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3049s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3049s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3049s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3049s     tapply, union, unique, unsplit, which.max, which.min
3049s 
3049s Loading required package: Biobase
3049s Welcome to Bioconductor
3049s 
3049s     Vignettes contain introductory material; view with
3049s     'browseVignettes()'. To cite Bioconductor, see
3049s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3049s 
3049s Loading required package: IRanges
3049s Loading required package: S4Vectors
3049s 
3049s Attaching package: ‘S4Vectors’
3049s 
3049s The following object is masked from ‘package:geneLenDataBase’:
3049s 
3049s     unfactor
3049s 
3049s The following object is masked from ‘package:utils’:
3049s 
3049s     findMatches
3049s 
3049s The following objects are masked from ‘package:base’:
3049s 
3049s     expand.grid, I, unname
3049s 
3053s Warning message:
3053s In pcls(G) : initial point very close to some inequality constraints
3053s Processing category: custom_list
3053s Using manually entered categories.
3053s Calculating the p-values...
3054s 'select()' returned 1:1 mapping between keys and columns
3055s 
3055s 
3055s Done.
3055s 
3055s 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 
3055s Loading required package: BiasedUrn
3055s Loading required package: geneLenDataBase
3066s 
3066s Loading required package: AnnotationDbi
3066s Loading required package: stats4
3066s Loading required package: BiocGenerics
3066s 
3066s Attaching package: ‘BiocGenerics’
3066s 
3066s The following objects are masked from ‘package:stats’:
3066s 
3066s     IQR, mad, sd, var, xtabs
3066s 
3066s The following objects are masked from ‘package:base’:
3066s 
3066s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3066s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3066s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3066s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3066s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3066s     tapply, union, unique, unsplit, which.max, which.min
3066s 
3066s Loading required package: Biobase
3066s Welcome to Bioconductor
3066s 
3066s     Vignettes contain introductory material; view with
3066s     'browseVignettes()'. To cite Bioconductor, see
3066s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3066s 
3066s Loading required package: IRanges
3066s Loading required package: S4Vectors
3066s 
3066s Attaching package: ‘S4Vectors’
3066s 
3066s The following object is masked from ‘package:geneLenDataBase’:
3066s 
3066s     unfactor
3066s 
3066s The following object is masked from ‘package:utils’:
3066s 
3066s     findMatches
3066s 
3066s The following objects are masked from ‘package:base’:
3066s 
3066s     expand.grid, I, unname
3066s 
3068s Warning message:
3068s In newton(lsp = lsp, X = G$X, y = G$y, Eb = G$Eb, UrS = G$UrS, L = G$L,  :
3068s   Iteration limit reached without full convergence - check carefully
3068s Processing category: custom_list
3068s Using manually entered categories.
3068s Calculating the p-values...
3068s 'select()' returned 1:1 mapping between keys and columns
3068s 
3068s 
3068s Done.
3068s 
3068s 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 
3069s Loading required package: BiasedUrn
3069s Loading required package: geneLenDataBase
3079s 
3079s Loading required package: AnnotationDbi
3079s Loading required package: stats4
3079s Loading required package: BiocGenerics
3079s 
3079s Attaching package: ‘BiocGenerics’
3079s 
3079s The following objects are masked from ‘package:stats’:
3079s 
3079s     IQR, mad, sd, var, xtabs
3079s 
3079s The following objects are masked from ‘package:base’:
3079s 
3079s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3079s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3079s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3079s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3079s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3079s     tapply, union, unique, unsplit, which.max, which.min
3079s 
3079s Loading required package: Biobase
3079s Welcome to Bioconductor
3079s 
3079s     Vignettes contain introductory material; view with
3079s     'browseVignettes()'. To cite Bioconductor, see
3079s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3079s 
3079s Loading required package: IRanges
3079s Loading required package: S4Vectors
3079s 
3079s Attaching package: ‘S4Vectors’
3079s 
3079s The following object is masked from ‘package:geneLenDataBase’:
3079s 
3079s     unfactor
3079s 
3079s The following object is masked from ‘package:utils’:
3079s 
3079s     findMatches
3079s 
3079s The following objects are masked from ‘package:base’:
3079s 
3079s     expand.grid, I, unname
3079s 
3081s Warning message:
3081s In newton(lsp = lsp, X = G$X, y = G$y, Eb = G$Eb, UrS = G$UrS, L = G$L,  :
3081s   Iteration limit reached without full convergence - check carefully
3081s Processing category: custom_list
3081s Using manually entered categories.
3081s Calculating the p-values...
3082s 'select()' returned 1:1 mapping between keys and columns
3082s 
3082s 
3082s Done.
3082s 
3082s 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 
3082s Loading required package: BiasedUrn
3082s Loading required package: geneLenDataBase
3092s 
3092s Loading required package: AnnotationDbi
3092s Loading required package: stats4
3092s Loading required package: BiocGenerics
3092s 
3092s Attaching package: ‘BiocGenerics’
3092s 
3092s The following objects are masked from ‘package:stats’:
3092s 
3092s     IQR, mad, sd, var, xtabs
3092s 
3092s The following objects are masked from ‘package:base’:
3092s 
3092s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3092s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3092s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3092s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3092s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3092s     tapply, union, unique, unsplit, which.max, which.min
3092s 
3092s Loading required package: Biobase
3092s Welcome to Bioconductor
3092s 
3092s     Vignettes contain introductory material; view with
3092s     'browseVignettes()'. To cite Bioconductor, see
3092s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3092s 
3092s Loading required package: IRanges
3092s Loading required package: S4Vectors
3092s 
3092s Attaching package: ‘S4Vectors’
3092s 
3092s The following object is masked from ‘package:geneLenDataBase’:
3092s 
3092s     unfactor
3092s 
3092s The following object is masked from ‘package:utils’:
3092s 
3092s     findMatches
3092s 
3092s The following objects are masked from ‘package:base’:
3092s 
3092s     expand.grid, I, unname
3092s 
3094s Processing category: custom_list
3094s Using manually entered categories.
3094s Calculating the p-values...
3094s 'select()' returned 1:1 mapping between keys and columns
3094s 
3094s 
3094s Done.
3094s 
3094s 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 
3095s Loading required package: BiasedUrn
3095s Loading required package: geneLenDataBase
3105s 
3105s Loading required package: AnnotationDbi
3105s Loading required package: stats4
3105s Loading required package: BiocGenerics
3105s 
3105s Attaching package: ‘BiocGenerics’
3105s 
3105s The following objects are masked from ‘package:stats’:
3105s 
3105s     IQR, mad, sd, var, xtabs
3105s 
3105s The following objects are masked from ‘package:base’:
3105s 
3105s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3105s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3105s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3105s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3105s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3105s     tapply, union, unique, unsplit, which.max, which.min
3105s 
3105s Loading required package: Biobase
3105s Welcome to Bioconductor
3105s 
3105s     Vignettes contain introductory material; view with
3105s     'browseVignettes()'. To cite Bioconductor, see
3105s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3105s 
3105s Loading required package: IRanges
3105s Loading required package: S4Vectors
3105s 
3105s Attaching package: ‘S4Vectors’
3105s 
3105s The following object is masked from ‘package:geneLenDataBase’:
3105s 
3105s     unfactor
3105s 
3105s The following object is masked from ‘package:utils’:
3105s 
3105s     findMatches
3105s 
3105s The following objects are masked from ‘package:base’:
3105s 
3105s     expand.grid, I, unname
3105s 
3107s Processing category: custom_list
3107s Using manually entered categories.
3107s Calculating the p-values...
3107s 'select()' returned 1:1 mapping between keys and columns
3107s 
3107s 
3107s Done.
3107s 
3107s 
3107s 
3107s ** Found 25 features as differentially expressed.
3107s 
3107s 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
3107s CMD: Rscript diffExpr.P0.001_C2.matrix.R
3107s Loading required package: BiocGenerics
3107s 
3107s Attaching package: ‘BiocGenerics’
3107s 
3107s The following objects are masked from ‘package:stats’:
3107s 
3107s     IQR, mad, sd, var, xtabs
3107s 
3107s The following objects are masked from ‘package:base’:
3107s 
3107s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
3107s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
3107s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
3107s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
3107s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
3107s     tapply, union, unique, unsplit, which.max, which.min
3107s 
3108s Welcome to Bioconductor
3108s 
3108s     Vignettes contain introductory material; view with
3108s     'browseVignettes()'. To cite Bioconductor, see
3108s     'citation("Biobase")', and for packages 'citation("pkgname")'.
3108s 
3108s 
3108s Attaching package: ‘fastcluster’
3108s 
3108s The following object is masked from ‘package:stats’:
3108s 
3108s     hclust
3108s 
3108s [1] "Reading matrix file."
3109s null device 
3109s           1 
3109s for plotting:: min.raw: -0.790731955608766 max.raw: 1
3109s for plotting:: min.raw: -9.76652141391246 max.raw: 9.76652141391246
3109s null device 
3109s           1 
3109s validating:  Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset 
3109s no DE entries reported here.
3109s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset) passes test.
3109s validating:  Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.heatshock-UP.subset 
3109s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_heatshock.edgeR.DE_results.P0.001_C2.heatshock-UP.subset) passes test.
3109s no DE entries reported here.
3109s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset) passes test.
3109s no DE entries reported here.
3109s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset) passes test.
3109s sampleA_mean:  351.239 
3109s sampleB_mean:  10243.92 
3109s num discordant:  0 
3109s validating:  Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset 
3109s validating:  Trinity_genes.counts.matrix.diauxic_shift_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset 
3109s validating:  Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset 
3109s sampleA_mean:  File: (Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.diauxic_shift-UP.subset) passes test.
3109s no DE entries reported here.
3109s File: (Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset) passes test.
3109s File: (Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.heatshock-UP.subset) passes test.
3109s File: (Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset) passes test.
3109s File: (Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.heatshock-UP.subset) passes test.
3109s no DE entries reported here.
3109s File: (Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset) passes test.
3109s File: (Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.log_growth-UP.subset) passes test.
3109s no DE entries reported here.
3109s File: (Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset) passes test.
3109s edgeR_genes/diffExpr.P0.001_C2.matrix, count: 26 DE features OK.
3109s 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.
3109s 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.
3109s 24474.99 
3109s sampleB_mean:  655.981 
3109s num discordant:  0 
3109s validating:  Trinity_genes.counts.matrix.diauxic_shift_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset 
3109s validating:  Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.heatshock-UP.subset 
3109s 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 
3109s 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 
3109s num discordant:  0 
3109s validating:  Trinity_genes.counts.matrix.heatshock_vs_log_growth.edgeR.DE_results.P0.001_C2.log_growth-UP.subset 
3109s sampleA_mean:  2036.649 135.207 
3109s sampleB_mean:  11080.21 1620.935 
3109s num discordant:  0 
3109s validating:  Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.heatshock-UP.subset 
3109s sampleA_mean:  7754.294 
3109s sampleB_mean:  252.38 
3109s num discordant:  0 
3109s validating:  Trinity_genes.counts.matrix.heatshock_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset 
3109s validating:  Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.log_growth-UP.subset 
3109s sampleA_mean:  9466.084 
3109s sampleB_mean:  470.915 
3109s num discordant:  0 
3109s validating:  Trinity_genes.counts.matrix.log_growth_vs_plateau.edgeR.DE_results.P0.001_C2.plateau-UP.subset 
3109s ./validate_results.pl 
3109s touch test
3109s make[2]: Leaving directory '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example'
3109s make[1]: Leaving directory '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis'
3109s Running example in test_align_and_estimate_abundance...
3109s make[1]: Entering directory '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance'
3109s Running example in PAIRED_END_ABUNDANCE_ESTIMATION...
3109s make[2]: Entering directory '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION'
3109s ../align_and_estimate_tester.pl RSEM "samples.txt" "../../test_DATA/Trinity.fasta"
3109s CMD: ln -sf ../../test_DATA/Trinity.fasta .
3109s CMD: /usr/lib/trinityrnaseq/util/align_and_estimate_abundance.pl --transcripts Trinity.fasta --prep_reference  --left /tmp/autopkgtest.xkSdGF/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.xkSdGF/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 
3109s CMD: /usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta > /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.gene_trans_map
3109s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.started
3109s CMD: bowtie2-build /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2
3109s Settings:
3109s   Output files: "/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.*.bt2"
3109s   Line rate: 6 (line is 64 bytes)
3109s   Lines per side: 1 (side is 64 bytes)
3109s   Offset rate: 4 (one in 16)
3109s   FTable chars: 10
3109s   Strings: unpacked
3109s   Max bucket size: default
3109s   Max bucket size, sqrt multiplier: default
3109s   Max bucket size, len divisor: 4
3109s   Difference-cover sample period: 1024
3109s   Endianness: little
3109s   Actual local endianness: little
3109s   Sanity checking: disabled
3109s   Assertions: disabled
3109s   Random seed: 0
3109s   Sizeofs: void*:8, int:4, long:8, size_t:8
3109s Input files DNA, FASTA:
3109s   /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta
3109s Reading reference sizes
3109s Building a SMALL index
3109s   Time reading reference sizes: 00:00:00
3109s Calculating joined length
3109s Writing header
3109s Reserving space for joined string
3109s Joining reference sequences
3109s   Time to join reference sequences: 00:00:00
3109s bmax according to bmaxDivN setting: 54360
3109s Using parameters --bmax 40770 --dcv 1024
3109s   Doing ahead-of-time memory usage test
3109s   Passed!  Constructing with these parameters: --bmax 40770 --dcv 1024
3109s Constructing suffix-array element generator
3109s Building DifferenceCoverSample
3109s   Building sPrime
3109s   Building sPrimeOrder
3109s   V-Sorting samples
3109s   V-Sorting samples time: 00:00:00
3109s   Allocating rank array
3109s   Ranking v-sort output
3109s   Ranking v-sort output time: 00:00:00
3109s   Invoking Larsson-Sadakane on ranks
3109s   Invoking Larsson-Sadakane on ranks time: 00:00:00
3109s   Sanity-checking and returning
3109s Building samples
3109s Reserving space for 12 sample suffixes
3109s Generating random suffixes
3109s QSorting 12 sample offsets, eliminating duplicates
3109s QSorting sample offsets, eliminating duplicates time: 00:00:00
3109s Multikey QSorting 12 samples
3109s   (Using difference cover)
3109s   Multikey QSorting samples time: 00:00:00
3109s Calculating bucket sizes
3109s Splitting and merging
3109s   Splitting and merging time: 00:00:00
3109s Split 2, merged 6; iterating...
3109s Splitting and merging
3109s   Splitting and merging time: 00:00:00
3109s Split 1, merged 2; iterating...
3109s Splitting and merging
3109s   Splitting and merging time: 00:00:00
3109s Split 1, merged 0; iterating...
3109s Splitting and merging
3109s   Splitting and merging time: 00:00:00
3109s Avg bucket size: 27179.5 (target: 40769)
3109s Converting suffix-array elements to index image
3109s Allocating ftab, absorbFtab
3109s Entering Ebwt loop
3109s Getting block 1 of 8
3109s   Reserving size (40770) for bucket 1
3109s   Calculating Z arrays for bucket 1
3109s   Entering block accumulator loop for bucket 1:
3109s   bucket 1: 10%
3109s   bucket 1: 20%
3109s   bucket 1: 30%
3109s   bucket 1: 40%
3109s   bucket 1: 50%
3109s   bucket 1: 60%
3109s   bucket 1: 70%
3109s   bucket 1: 80%
3109s   bucket 1: 90%
3109s   bucket 1: 100%
3109s   Sorting block of length 34231 for bucket 1
3109s   (Using difference cover)
3109s   Sorting block time: 00:00:00
3109s Returning block of 34232 for bucket 1
3109s Getting block 2 of 8
3109s   Reserving size (40770) for bucket 2
3109s   Calculating Z arrays for bucket 2
3109s   Entering block accumulator loop for bucket 2:
3109s   bucket 2: 10%
3109s   bucket 2: 20%
3109s   bucket 2: 30%
3109s   bucket 2: 40%
3109s   bucket 2: 50%
3109s   bucket 2: 60%
3109s   bucket 2: 70%
3109s   bucket 2: 80%
3109s   bucket 2: 90%
3109s   bucket 2: 100%
3109s   Sorting block of length 39793 for bucket 2
3109s   (Using difference cover)
3109s   Sorting block time: 00:00:00
3109s Returning block of 39794 for bucket 2
3109s Getting block 3 of 8
3109s   Reserving size (40770) for bucket 3
3109s   Calculating Z arrays for bucket 3
3109s   Entering block accumulator loop for bucket 3:
3109s   bucket 3: 10%
3109s   bucket 3: 20%
3109s   bucket 3: 30%
3109s   bucket 3: 40%
3109s   bucket 3: 50%
3109s   bucket 3: 60%
3109s   bucket 3: 70%
3109s   bucket 3: 80%
3109s   bucket 3: 90%
3109s   bucket 3: 100%
3109s   Sorting block of length 9793 for bucket 3
3109s   (Using difference cover)
3109s   Sorting block time: 00:00:00
3109s Returning block of 9794 for bucket 3
3109s Getting block 4 of 8
3109s   Reserving size (40770) for bucket 4
3109s   Calculating Z arrays for bucket 4
3109s   Entering block accumulator loop for bucket 4:
3109s   bucket 4: 10%
3109s   bucket 4: 20%
3109s   bucket 4: 30%
3109s   bucket 4: 40%
3109s   bucket 4: 50%
3109s   bucket 4: 60%
3109s   bucket 4: 70%
3109s   bucket 4: 80%
3109s   bucket 4: 90%
3109s   bucket 4: 100%
3109s   Sorting block of length 31901 for bucket 4
3109s   (Using difference cover)
3109s   Sorting block time: 00:00:00
3109s Returning block of 31902 for bucket 4
3109s Getting block 5 of 8
3109s   Reserving size (40770) for bucket 5
3109s   Calculating Z arrays for bucket 5
3109s   Entering block accumulator loop for bucket 5:
3109s   bucket 5: 10%
3109s   bucket 5: 20%
3109s   bucket 5: 30%
3109s   bucket 5: 40%
3109s   bucket 5: 50%
3109s   bucket 5: 60%
3109s   bucket 5: 70%
3109s   bucket 5: 80%
3109s   bucket 5: 90%
3109s   bucket 5: 100%
3109s   Sorting block of length 10600 for bucket 5
3109s   (Using difference cover)
3109s   Sorting block time: 00:00:00
3109s Returning block of 10601 for bucket 5
3109s Getting block 6 of 8
3109s   Reserving size (40770) for bucket 6
3109s   Calculating Z arrays for bucket 6
3109s   Entering block accumulator loop for bucket 6:
3109s   bucket 6: 10%
3109s   bucket 6: 20%
3109s   bucket 6: 30%
3109s   bucket 6: 40%
3109s   bucket 6: 50%
3109s   bucket 6: 60%
3109s   bucket 6: 70%
3109s   bucket 6: 80%
3109s   bucket 6: 90%
3109s   bucket 6: 100%
3109s   Sorting block of length 40652 for bucket 6
3109s   (Using difference cover)
3109s   Sorting block time: 00:00:00
3109s Returning block of 40653 for bucket 6
3109s Getting block 7 of 8
3109s   Reserving size (40770) for bucket 7
3109s   Calculating Z arrays for bucket 7
3109s   Entering block accumulator loop for bucket 7:
3109s   bucket 7: 10%
3109s   bucket 7: 20%
3109s   bucket 7: 30%
3109s   bucket 7: 40%
3109s   bucket 7: 50%
3109s   bucket 7: 60%
3109s   bucket 7: 70%
3109s   bucket 7: 80%
3109s   bucket 7: 90%
3109s   bucket 7: 100%
3109s   Sorting block of length 18337 for bucket 7
3109s   (Using difference cover)
3109s   Sorting block time: 00:00:00
3109s Returning block of 18338 for bucket 7
3109s Getting block 8 of 8
3109s   Reserving size (40770) for bucket 8
3109s   Calculating Z arrays for bucket 8
3109s   Entering block accumulator loop for bucket 8:
3109s   bucket 8: 10%
3109s   bucket 8: 20%
3109s   bucket 8: 30%
3109s   bucket 8: 40%
3109s   bucket 8: 50%
3109s   bucket 8: 60%
3109s   bucket 8: 70%
3109s   bucket 8: 80%
3109s   bucket 8: 90%
3109s   bucket 8: 100%
3109s   Sorting block of length 32129 for bucket 8
3109s   (Using difference cover)
3109s   Sorting block time: 00:00:00
3109s Returning block of 32130 for bucket 8
3109s Exited Ebwt loop
3109s fchr[A]: 0
3109s fchr[C]: 59864
3109s fchr[G]: 108205
3109s fchr[T]: 157829
3109s fchr[$]: 217443
3109s Exiting Ebwt::buildToDisk()
3109s Returning from initFromVector
3109s Wrote 4313663 bytes to primary EBWT file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.1.bt2.tmp
3109s Wrote 54368 bytes to secondary EBWT file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.2.bt2.tmp
3109s Re-opening _in1 and _in2 as input streams
3109s Returning from Ebwt constructor
3109s Headers:
3109s     len: 217443
3109s     bwtLen: 217444
3109s     sz: 54361
3109s     bwtSz: 54361
3109s     lineRate: 6
3109s     offRate: 4
3109s     offMask: 0xfffffff0
3109s     ftabChars: 10
3109s     eftabLen: 20
3109s     eftabSz: 80
3109s     ftabLen: 1048577
3109s     ftabSz: 4194308
3109s     offsLen: 13591
3109s     offsSz: 54364
3109s     lineSz: 64
3109s     sideSz: 64
3109s     sideBwtSz: 48
3109s     sideBwtLen: 192
3109s     numSides: 1133
3109s     numLines: 1133
3109s     ebwtTotLen: 72512
3109s     ebwtTotSz: 72512
3109s     color: 0
3109s     reverse: 0
3109s Total time for call to driver() for forward index: 00:00:00
3109s Reading reference sizes
3109s   Time reading reference sizes: 00:00:00
3109s Calculating joined length
3109s Writing header
3109s Reserving space for joined string
3109s Joining reference sequences
3109s   Time to join reference sequences: 00:00:00
3109s   Time to reverse reference sequence: 00:00:00
3109s bmax according to bmaxDivN setting: 54360
3109s Using parameters --bmax 40770 --dcv 1024
3109s   Doing ahead-of-time memory usage test
3109s   Passed!  Constructing with these parameters: --bmax 40770 --dcv 1024
3109s Constructing suffix-array element generator
3109s Building DifferenceCoverSample
3109s   Building sPrime
3109s   Building sPrimeOrder
3109s   V-Sorting samples
3109s   V-Sorting samples time: 00:00:00
3109s   Allocating rank array
3109s   Ranking v-sort output
3109s   Ranking v-sort output time: 00:00:00
3109s   Invoking Larsson-Sadakane on ranks
3109s   Invoking Larsson-Sadakane on ranks time: 00:00:00
3109s   Sanity-checking and returning
3109s Building samples
3109s Reserving space for 12 sample suffixes
3109s Generating random suffixes
3109s QSorting 12 sample offsets, eliminating duplicates
3109s QSorting sample offsets, eliminating duplicates time: 00:00:00
3109s Multikey QSorting 12 samples
3109s   (Using difference cover)
3109s   Multikey QSorting samples time: 00:00:00
3109s Calculating bucket sizes
3109s Splitting and merging
3109s   Splitting and merging time: 00:00:00
3109s Split 1, merged 6; iterating...
3109s Splitting and merging
3109s   Splitting and merging time: 00:00:00
3109s Avg bucket size: 31062.4 (target: 40769)
3109s Converting suffix-array elements to index image
3109s Allocating ftab, absorbFtab
3109s Entering Ebwt loop
3109s Getting block 1 of 7
3109s   Reserving size (40770) for bucket 1
3109s   Calculating Z arrays for bucket 1
3109s   Entering block accumulator loop for bucket 1:
3109s   bucket 1: 10%
3109s   bucket 1: 20%
3109s   bucket 1: 30%
3109s   bucket 1: 40%
3109s   bucket 1: 50%
3109s   bucket 1: 60%
3109s   bucket 1: 70%
3109s   bucket 1: 80%
3109s   bucket 1: 90%
3109s   bucket 1: 100%
3109s   Sorting block of length 37058 for bucket 1
3109s   (Using difference cover)
3109s   Sorting block time: 00:00:00
3109s Returning block of 37059 for bucket 1
3109s Getting block 2 of 7
3109s   Reserving size (40770) for bucket 2
3109s   Calculating Z arrays for bucket 2
3109s   Entering block accumulator loop for bucket 2:
3109s   bucket 2: 10%
3109s   bucket 2: 20%
3109s   bucket 2: 30%
3109s   bucket 2: 40%
3109s   bucket 2: 50%
3109s   bucket 2: 60%
3109s   bucket 2: 70%
3109s   bucket 2: 80%
3109s   bucket 2: 90%
3109s   bucket 2: 100%
3109s   Sorting block of length 17846 for bucket 2
3109s   (Using difference cover)
3109s   Sorting block time: 00:00:00
3109s Returning block of 17847 for bucket 2
3110s Getting block 3 of 7
3110s   Reserving size (40770) for bucket 3
3110s   Calculating Z arrays for bucket 3
3110s   Entering block accumulator loop for bucket 3:
3110s   bucket 3: 10%
3110s   bucket 3: 20%
3110s   bucket 3: 30%
3110s   bucket 3: 40%
3110s   bucket 3: 50%
3110s   bucket 3: 60%
3110s   bucket 3: 70%
3110s   bucket 3: 80%
3110s   bucket 3: 90%
3110s   bucket 3: 100%
3110s   Sorting block of length 39327 for bucket 3
3110s   (Using difference cover)
3110s   Sorting block time: 00:00:00
3110s Returning block of 39328 for bucket 3
3110s Getting block 4 of 7
3110s   Reserving size (40770) for bucket 4
3110s   Calculating Z arrays for bucket 4
3110s   Entering block accumulator loop for bucket 4:
3110s   bucket 4: 10%
3110s   bucket 4: 20%
3110s   bucket 4: 30%
3110s   bucket 4: 40%
3110s   bucket 4: 50%
3110s   bucket 4: 60%
3110s   bucket 4: 70%
3110s   bucket 4: 80%
3110s   bucket 4: 90%
3110s   bucket 4: 100%
3110s   Sorting block of length 34139 for bucket 4
3110s   (Using difference cover)
3110s   Sorting block time: 00:00:00
3110s Returning block of 34140 for bucket 4
3110s Getting block 5 of 7
3110s   Reserving size (40770) for bucket 5
3110s   Calculating Z arrays for bucket 5
3110s   Entering block accumulator loop for bucket 5:
3110s   bucket 5: 10%
3110s   bucket 5: 20%
3110s   bucket 5: 30%
3110s   bucket 5: 40%
3110s   bucket 5: 50%
3110s   bucket 5: 60%
3110s   bucket 5: 70%
3110s   bucket 5: 80%
3110s   bucket 5: 90%
3110s   bucket 5: 100%
3110s   Sorting block of length 31038 for bucket 5
3110s   (Using difference cover)
3110s   Sorting block time: 00:00:00
3110s Returning block of 31039 for bucket 5
3110s Getting block 6 of 7
3110s   Reserving size (40770) for bucket 6
3110s   Calculating Z arrays for bucket 6
3110s   Entering block accumulator loop for bucket 6:
3110s   bucket 6: 10%
3110s   bucket 6: 20%
3110s   bucket 6: 30%
3110s   bucket 6: 40%
3110s   bucket 6: 50%
3110s   bucket 6: 60%
3110s   bucket 6: 70%
3110s   bucket 6: 80%
3110s   bucket 6: 90%
3110s   bucket 6: 100%
3110s   Sorting block of length 21215 for bucket 6
3110s   (Using difference cover)
3110s   Sorting block time: 00:00:01
3110s Returning block of 21216 for bucket 6
3110s Getting block 7 of 7
3110s   Reserving size (40770) for bucket 7
3110s   Calculating Z arrays for bucket 7
3110s   Entering block accumulator loop for bucket 7:
3110s   bucket 7: 10%
3110s   bucket 7: 20%
3110s   bucket 7: 30%
3110s   bucket 7: 40%
3110s   bucket 7: 50%
3110s   bucket 7: 60%
3110s   bucket 7: 70%
3110s   bucket 7: 80%
3110s   bucket 7: 90%
3110s   bucket 7: 100%
3110s   Sorting block of length 36814 for bucket 7
3110s   (Using difference cover)
3110s   Sorting block time: 00:00:00
3110s Returning block of 36815 for bucket 7
3110s Exited Ebwt loop
3110s fchr[A]: 0
3110s fchr[C]: 59864
3110s fchr[G]: 108205
3110s fchr[T]: 157829
3110s fchr[$]: 217443
3110s Exiting Ebwt::buildToDisk()
3110s Returning from initFromVector
3110s Wrote 4313663 bytes to primary EBWT file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.1.bt2.tmp
3110s Wrote 54368 bytes to secondary EBWT file: /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.2.bt2.tmp
3110s Re-opening _in1 and _in2 as input streams
3110s Returning from Ebwt constructor
3110s Headers:
3110s     len: 217443
3110s     bwtLen: 217444
3110s     sz: 54361
3110s     bwtSz: 54361
3110s     lineRate: 6
3110s     offRate: 4
3110s     offMask: 0xfffffff0
3110s     ftabChars: 10
3110s     eftabLen: 20
3110s     eftabSz: 80
3110s     ftabLen: 1048577
3110s     ftabSz: 4194308
3110s     offsLen: 13591
3110s     offsSz: 54364
3110s     lineSz: 64
3110s     sideSz: 64
3110s     sideBwtSz: 48
3110s     sideBwtLen: 192
3110s     numSides: 1133
3110s     numLines: 1133
3110s     ebwtTotLen: 72512
3110s     ebwtTotSz: 72512
3110s     color: 0
3110s     reverse: 1
3110s Total time for backward call to driver() for mirror index: 00:00:01
3110s Renaming /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.3.bt2
3110s Renaming /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.4.bt2
3110s Renaming /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.1.bt2
3110s Renaming /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.2.bt2
3110s Renaming /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.1.bt2
3110s Renaming /tmp/autopkgtest.xkSdGF/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.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2.rev.2.bt2
3110s CMD: touch /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.rsem.prepped.started
3110s CMD: rsem-prepare-reference  --transcript-to-gene-map /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.gene_trans_map /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM
3110s rsem-synthesis-reference-transcripts /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM 0 1 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.gene_trans_map /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta
3110s Transcript Information File is generated!
3110s Group File is generated!
3110s Extracted Sequences File is generated!
3110s 
3110s rsem-preref /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.transcripts.fa 1 /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM
3110s Refs.makeRefs finished!
3110s Refs.saveRefs finished!
3110s /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.idx.fa is generated!
3110s /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.RSEM.n2g.idx.fa is generated!
3110s 
3110s $VAR1 = [
3110s           {
3110s             'left' => '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.left.fq.gz',
3110s             'output_dir' => 'RSEM-heatshock',
3110s             'right' => '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/../../test_DATA/Sp_hs.10k.right.fq.gz'
3110s           }
3110s         ];
3110s CMD: set -o pipefail && bowtie2 --no-mixed --no-discordant --gbar 1000 --end-to-end -k 200  -q -X 800 -x /tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Trinity.fasta.bowtie2 -1 /tmp/autopkgtest.xkSdGF/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.xkSdGF/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 
3111s 10000 reads; of these:
3111s   10000 (100.00%) were paired; of these:
3111s     7088 (70.88%) aligned concordantly 0 times
3111s     1764 (17.64%) aligned concordantly exactly 1 time
3111s     1148 (11.48%) aligned concordantly >1 times
3111s 29.12% overall alignment rate
3111s [bam_sort_core] merging from 0 files and 4 in-memory blocks...
3111s CMD: touch bowtie2.bam.ok
3111s CMD: convert-sam-for-rsem -p 4 bowtie2.bam bowtie2.bam.for_rsem
3111s samtools sort -n -@ 4 -m 1G -o bowtie2.bam.for_rsem.tmp.bam bowtie2.bam
3111s samtools sort: couldn't allocate memory for bam_mem
3111s 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.
3111s Error, cmd:
3111s /usr/lib/trinityrnaseq/util/align_and_estimate_abundance.pl --transcripts Trinity.fasta --prep_reference  --left /tmp/autopkgtest.xkSdGF/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.xkSdGF/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 
3111s  died with ret (512) at /usr/lib/trinityrnaseq/PerlLib/Process_cmd.pm line 19.
3111s 	Process_cmd::process_cmd("/usr/lib/trinityrnaseq/util/align_and_estimate_abundance.pl -"...) called at ../align_and_estimate_tester.pl line 98
3111s make[2]: *** [Makefile:25: test_RSEM] Error 2
3111s make[1]: *** [Makefile:8: test] Error 2
3111s make: *** [Makefile:18: test] Error 2
3111s "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!
3111s make[2]: Leaving directory '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION'
3111s make[1]: Leaving directory '/tmp/autopkgtest.xkSdGF/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance'
3111s autopkgtest [11:00:26]: test run-tests: -----------------------]
3112s run-tests            FAIL non-zero exit status 2
3112s autopkgtest [11:00:27]: test run-tests:  - - - - - - - - - - results - - - - - - - - - -
3113s autopkgtest [11:00:28]: @@@@@@@@@@@@@@@@@@@@ summary
3113s run-tests            FAIL non-zero exit status 2
3121s nova [W] Skipping flock in bos03-arm64
3121s Creating nova instance adt-plucky-arm64-trinityrnaseq-20241101-100834-juju-7f2275-prod-proposed-migration-environment-2-1c5a00f7-79e8-47f1-8fcb-e9b5e3707bd8 from image adt/ubuntu-plucky-arm64-server-20241101.img (UUID 520a937f-514a-4e80-b76b-163a8c247e3e)...